Output - UPHL-BioNGS/Cecret GitHub Wiki
Cecret produces a lot of files. Most of these files are in the format of {params.outdir}/{process}/{resultant files from that process}.
Final File Tree after running cecret.nf
cecret/
├── aligned
│ ├── ERR5181310.sorted.bam
│ ├── ERR5181310.sorted.bam.bai
│ ├── ERR5181360.sorted.bam
│ ├── ERR5181360.sorted.bam.bai
│ ├── ERR5405022.sorted.bam
│ ├── ERR5405022.sorted.bam.bai
│ ├── ERR5556343.sorted.bam
│ ├── ERR5556343.sorted.bam.bai
│ ├── ERR5691945.sorted.bam
│ ├── ERR5691945.sorted.bam.bai
│ ├── ERR5743043.sorted.bam
│ ├── ERR5743043.sorted.bam.bai
│ ├── ERR5743893.sorted.bam
│ ├── ERR5743893.sorted.bam.bai
│ ├── ERR5749609.sorted.bam
│ ├── ERR5749609.sorted.bam.bai
│ ├── ERR5771988.sorted.bam
│ ├── ERR5771988.sorted.bam.bai
│ ├── SRR13422799.sorted.bam
│ ├── SRR13422799.sorted.bam.bai
│ ├── SRR13422802.sorted.bam
│ ├── SRR13422802.sorted.bam.bai
│ ├── SRR13500958.sorted.bam
│ ├── SRR13500958.sorted.bam.bai
│ ├── SRR13511054.sorted.bam
│ ├── SRR13511054.sorted.bam.bai
│ ├── SRR13603869.sorted.bam
│ ├── SRR13603869.sorted.bam.bai
│ ├── SRR13606410.sorted.bam
│ ├── SRR13606410.sorted.bam.bai
│ ├── SRR14241199.sorted.bam
│ └── SRR14241199.sorted.bam.bai
├── bcftools_variants
│ ├── ERR5181310.vcf
│ ├── ERR5181360.vcf
│ ├── ERR5405022.vcf
│ ├── ERR5556343.vcf
│ ├── ERR5691945.vcf
│ ├── ERR5743043.vcf
│ ├── ERR5743893.vcf
│ ├── ERR5749609.vcf
│ ├── ERR5771988.vcf
│ ├── SRR13422799.vcf
│ ├── SRR13422802.vcf
│ ├── SRR13500958.vcf
│ ├── SRR13511054.vcf
│ ├── SRR13603869.vcf
│ ├── SRR13606410.vcf
│ └── SRR14241199.vcf
├── cecret_results.csv
├── cecret_results.txt
├── consensus
│ ├── ERR5181310.consensus.fa
│ ├── ERR5181360.consensus.fa
│ ├── ERR5405022.consensus.fa
│ ├── ERR5556343.consensus.fa
│ ├── ERR5691945.consensus.fa
│ ├── ERR5743043.consensus.fa
│ ├── ERR5743893.consensus.fa
│ ├── ERR5749609.consensus.fa
│ ├── ERR5771988.consensus.fa
│ ├── SRR13422799.consensus.fa
│ ├── SRR13422802.consensus.fa
│ ├── SRR13500958.consensus.fa
│ ├── SRR13511054.consensus.fa
│ ├── SRR13603869.consensus.fa
│ ├── SRR13606410.consensus.fa
│ └── SRR14241199.consensus.fa
├── dataset
│ ├── CHANGELOG.md
│ ├── genome_annotation.gff3
│ ├── pathogen.json
│ ├── README.md
│ ├── reference.fasta
│ ├── sequences.fasta
│ └── tree.json
├── fastqc
│ ├── ERR5181310_1_fastqc.html
│ ├── ERR5181310_1_fastqc.zip
│ ├── ERR5181310_2_fastqc.html
│ ├── ERR5181310_2_fastqc.zip
│ ├── ERR5181310_fastq_name.csv
│ ├── ERR5181360_1_fastqc.html
│ ├── ERR5181360_1_fastqc.zip
│ ├── ERR5181360_2_fastqc.html
│ ├── ERR5181360_2_fastqc.zip
│ ├── ERR5181360_fastq_name.csv
│ ├── ERR5405022_1_fastqc.html
│ ├── ERR5405022_1_fastqc.zip
│ ├── ERR5405022_2_fastqc.html
│ ├── ERR5405022_2_fastqc.zip
│ ├── ERR5405022_fastq_name.csv
│ ├── ERR5556343_1_fastqc.html
│ ├── ERR5556343_1_fastqc.zip
│ ├── ERR5556343_2_fastqc.html
│ ├── ERR5556343_2_fastqc.zip
│ ├── ERR5556343_fastq_name.csv
│ ├── ERR5691945_1_fastqc.html
│ ├── ERR5691945_1_fastqc.zip
│ ├── ERR5691945_2_fastqc.html
│ ├── ERR5691945_2_fastqc.zip
│ ├── ERR5691945_fastq_name.csv
│ ├── ERR5743043_1_fastqc.html
│ ├── ERR5743043_1_fastqc.zip
│ ├── ERR5743043_2_fastqc.html
│ ├── ERR5743043_2_fastqc.zip
│ ├── ERR5743043_fastq_name.csv
│ ├── ERR5743893_1_fastqc.html
│ ├── ERR5743893_1_fastqc.zip
│ ├── ERR5743893_2_fastqc.html
│ ├── ERR5743893_2_fastqc.zip
│ ├── ERR5743893_fastq_name.csv
│ ├── ERR5749609_1_fastqc.html
│ ├── ERR5749609_1_fastqc.zip
│ ├── ERR5749609_2_fastqc.html
│ ├── ERR5749609_2_fastqc.zip
│ ├── ERR5749609_fastq_name.csv
│ ├── ERR5771988_1_fastqc.html
│ ├── ERR5771988_1_fastqc.zip
│ ├── ERR5771988_2_fastqc.html
│ ├── ERR5771988_2_fastqc.zip
│ ├── ERR5771988_fastq_name.csv
│ ├── SRR13422799_1_fastqc.html
│ ├── SRR13422799_1_fastqc.zip
│ ├── SRR13422799_2_fastqc.html
│ ├── SRR13422799_2_fastqc.zip
│ ├── SRR13422799_fastq_name.csv
│ ├── SRR13422802_1_fastqc.html
│ ├── SRR13422802_1_fastqc.zip
│ ├── SRR13422802_2_fastqc.html
│ ├── SRR13422802_2_fastqc.zip
│ ├── SRR13422802_fastq_name.csv
│ ├── SRR13500958_1_fastqc.html
│ ├── SRR13500958_1_fastqc.zip
│ ├── SRR13500958_2_fastqc.html
│ ├── SRR13500958_2_fastqc.zip
│ ├── SRR13500958_fastq_name.csv
│ ├── SRR13511054_1_fastqc.html
│ ├── SRR13511054_1_fastqc.zip
│ ├── SRR13511054_2_fastqc.html
│ ├── SRR13511054_2_fastqc.zip
│ ├── SRR13511054_fastq_name.csv
│ ├── SRR13603869_1_fastqc.html
│ ├── SRR13603869_1_fastqc.zip
│ ├── SRR13603869_2_fastqc.html
│ ├── SRR13603869_2_fastqc.zip
│ ├── SRR13603869_fastq_name.csv
│ ├── SRR13606410_1_fastqc.html
│ ├── SRR13606410_1_fastqc.zip
│ ├── SRR13606410_2_fastqc.html
│ ├── SRR13606410_2_fastqc.zip
│ ├── SRR13606410_fastq_name.csv
│ ├── SRR14241199_1_fastqc.html
│ ├── SRR14241199_1_fastqc.zip
│ ├── SRR14241199_2_fastqc.html
│ ├── SRR14241199_2_fastqc.zip
│ └── SRR14241199_fastq_name.csv
├── freyja
│ ├── aggregated-freyja.png
│ ├── aggregated-freyja.tsv
│ ├── ERR5181310_demix.tsv
│ ├── ERR5181310_depths.tsv
│ ├── ERR5181310_freyja_lineages_mqc.png
│ ├── ERR5181310_freyja_lineages.png
│ ├── ERR5181310_variants.tsv
│ ├── ERR5181360_demix.tsv
│ ├── ERR5181360_depths.tsv
│ ├── ERR5181360_freyja_lineages_mqc.png
│ ├── ERR5181360_freyja_lineages.png
│ ├── ERR5181360_variants.tsv
│ ├── ERR5405022_demix.tsv
│ ├── ERR5405022_depths.tsv
│ ├── ERR5405022_freyja_lineages_mqc.png
│ ├── ERR5405022_freyja_lineages.png
│ ├── ERR5405022_variants.tsv
│ ├── ERR5556343_demix.tsv
│ ├── ERR5556343_depths.tsv
│ ├── ERR5556343_freyja_lineages_mqc.png
│ ├── ERR5556343_freyja_lineages.png
│ ├── ERR5556343_variants.tsv
│ ├── ERR5691945_demix.tsv
│ ├── ERR5691945_depths.tsv
│ ├── ERR5691945_freyja_lineages_mqc.png
│ ├── ERR5691945_freyja_lineages.png
│ ├── ERR5691945_variants.tsv
│ ├── ERR5743043_demix.tsv
│ ├── ERR5743043_depths.tsv
│ ├── ERR5743043_freyja_lineages_mqc.png
│ ├── ERR5743043_freyja_lineages.png
│ ├── ERR5743043_variants.tsv
│ ├── ERR5743893_demix.tsv
│ ├── ERR5743893_depths.tsv
│ ├── ERR5743893_freyja_lineages_mqc.png
│ ├── ERR5743893_freyja_lineages.png
│ ├── ERR5743893_variants.tsv
│ ├── ERR5749609_demix.tsv
│ ├── ERR5749609_depths.tsv
│ ├── ERR5749609_freyja_lineages_mqc.png
│ ├── ERR5749609_freyja_lineages.png
│ ├── ERR5749609_variants.tsv
│ ├── ERR5771988_demix.tsv
│ ├── ERR5771988_depths.tsv
│ ├── ERR5771988_freyja_lineages_mqc.png
│ ├── ERR5771988_freyja_lineages.png
│ ├── ERR5771988_variants.tsv
│ ├── SRR13422799_demix.tsv
│ ├── SRR13422799_depths.tsv
│ ├── SRR13422799_freyja_lineages_mqc.png
│ ├── SRR13422799_freyja_lineages.png
│ ├── SRR13422799_variants.tsv
│ ├── SRR13422802_demix.tsv
│ ├── SRR13422802_depths.tsv
│ ├── SRR13422802_freyja_lineages_mqc.png
│ ├── SRR13422802_freyja_lineages.png
│ ├── SRR13422802_variants.tsv
│ ├── SRR13500958_demix.tsv
│ ├── SRR13500958_depths.tsv
│ ├── SRR13500958_freyja_lineages_mqc.png
│ ├── SRR13500958_freyja_lineages.png
│ ├── SRR13500958_variants.tsv
│ ├── SRR13511054_demix.tsv
│ ├── SRR13511054_depths.tsv
│ ├── SRR13511054_freyja_lineages_mqc.png
│ ├── SRR13511054_freyja_lineages.png
│ ├── SRR13511054_variants.tsv
│ ├── SRR13603869_demix.tsv
│ ├── SRR13603869_depths.tsv
│ ├── SRR13603869_freyja_lineages_mqc.png
│ ├── SRR13603869_freyja_lineages.png
│ ├── SRR13603869_variants.tsv
│ ├── SRR13606410_demix.tsv
│ ├── SRR13606410_depths.tsv
│ ├── SRR13606410_freyja_lineages_mqc.png
│ ├── SRR13606410_freyja_lineages.png
│ ├── SRR13606410_variants.tsv
│ ├── SRR14241199_demix.tsv
│ ├── SRR14241199_depths.tsv
│ ├── SRR14241199_freyja_lineages_mqc.png
│ ├── SRR14241199_freyja_lineages.png
│ └── SRR14241199_variants.tsv
├── heatcluster
│ ├── heatcluster.png
│ └── sorted_matrix.csv
├── iqtree2
│ ├── iqtree2.iqtree
│ ├── iqtree2.log
│ ├── iqtree2.mldist
│ ├── iqtree2.treefile
│ └── iqtree2.treefile.nwk
├── ivar_consensus
│ ├── ERR5181310.consensus.fa
│ ├── ERR5181310.consensus.qual.txt
│ ├── ERR5181360.consensus.fa
│ ├── ERR5181360.consensus.qual.txt
│ ├── ERR5405022.consensus.fa
│ ├── ERR5405022.consensus.qual.txt
│ ├── ERR5556343.consensus.fa
│ ├── ERR5556343.consensus.qual.txt
│ ├── ERR5691945.consensus.fa
│ ├── ERR5691945.consensus.qual.txt
│ ├── ERR5743043.consensus.fa
│ ├── ERR5743043.consensus.qual.txt
│ ├── ERR5743893.consensus.fa
│ ├── ERR5743893.consensus.qual.txt
│ ├── ERR5749609.consensus.fa
│ ├── ERR5749609.consensus.qual.txt
│ ├── ERR5771988.consensus.fa
│ ├── ERR5771988.consensus.qual.txt
│ ├── SRR13422799.consensus.fa
│ ├── SRR13422799.consensus.qual.txt
│ ├── SRR13422802.consensus.fa
│ ├── SRR13422802.consensus.qual.txt
│ ├── SRR13500958.consensus.fa
│ ├── SRR13500958.consensus.qual.txt
│ ├── SRR13511054.consensus.fa
│ ├── SRR13511054.consensus.qual.txt
│ ├── SRR13603869.consensus.fa
│ ├── SRR13603869.consensus.qual.txt
│ ├── SRR13606410.consensus.fa
│ ├── SRR13606410.consensus.qual.txt
│ ├── SRR14241199.consensus.fa
│ └── SRR14241199.consensus.qual.txt
├── ivar_trim
│ ├── ERR5181310_ivar.log
│ ├── ERR5181310.primertrim.sorted.bam
│ ├── ERR5181310.primertrim.sorted.bam.bai
│ ├── ERR5181360_ivar.log
│ ├── ERR5181360.primertrim.sorted.bam
│ ├── ERR5181360.primertrim.sorted.bam.bai
│ ├── ERR5405022_ivar.log
│ ├── ERR5405022.primertrim.sorted.bam
│ ├── ERR5405022.primertrim.sorted.bam.bai
│ ├── ERR5556343_ivar.log
│ ├── ERR5556343.primertrim.sorted.bam
│ ├── ERR5556343.primertrim.sorted.bam.bai
│ ├── ERR5691945_ivar.log
│ ├── ERR5691945.primertrim.sorted.bam
│ ├── ERR5691945.primertrim.sorted.bam.bai
│ ├── ERR5743043_ivar.log
│ ├── ERR5743043.primertrim.sorted.bam
│ ├── ERR5743043.primertrim.sorted.bam.bai
│ ├── ERR5743893_ivar.log
│ ├── ERR5743893.primertrim.sorted.bam
│ ├── ERR5743893.primertrim.sorted.bam.bai
│ ├── ERR5749609_ivar.log
│ ├── ERR5749609.primertrim.sorted.bam
│ ├── ERR5749609.primertrim.sorted.bam.bai
│ ├── ERR5771988_ivar.log
│ ├── ERR5771988.primertrim.sorted.bam
│ ├── ERR5771988.primertrim.sorted.bam.bai
│ ├── SRR13422799_ivar.log
│ ├── SRR13422799.primertrim.sorted.bam
│ ├── SRR13422799.primertrim.sorted.bam.bai
│ ├── SRR13422802_ivar.log
│ ├── SRR13422802.primertrim.sorted.bam
│ ├── SRR13422802.primertrim.sorted.bam.bai
│ ├── SRR13500958_ivar.log
│ ├── SRR13500958.primertrim.sorted.bam
│ ├── SRR13500958.primertrim.sorted.bam.bai
│ ├── SRR13511054_ivar.log
│ ├── SRR13511054.primertrim.sorted.bam
│ ├── SRR13511054.primertrim.sorted.bam.bai
│ ├── SRR13603869_ivar.log
│ ├── SRR13603869.primertrim.sorted.bam
│ ├── SRR13603869.primertrim.sorted.bam.bai
│ ├── SRR13606410_ivar.log
│ ├── SRR13606410.primertrim.sorted.bam
│ ├── SRR13606410.primertrim.sorted.bam.bai
│ ├── SRR14241199_ivar.log
│ ├── SRR14241199.primertrim.sorted.bam
│ └── SRR14241199.primertrim.sorted.bam.bai
├── logs
│ └── CECRET:SUBWORKFLOW:PROCESS
│ └── CECRET:SUBWORKFLOW:PROCESS.*.log
├── mafft
│ ├── mafft_aligned.fasta
│ └── ultimate.fasta
├── multiqc
│ ├── multiqc_data
│ │ ├── fastqc_adapter_content_plot.txt
│ │ ├── fastqc_overrepresented_sequences_plot.txt
│ │ ├── fastqc_per_base_n_content_plot.txt
│ │ ├── fastqc_per_base_sequence_quality_plot.txt
│ │ ├── fastqc_per_sequence_gc_content_plot_Counts.txt
│ │ ├── fastqc_per_sequence_gc_content_plot_Percentages.txt
│ │ ├── fastqc_per_sequence_quality_scores_plot.txt
│ │ ├── fastqc_sequence_counts_plot.txt
│ │ ├── fastqc_sequence_duplication_levels_plot.txt
│ │ ├── fastqc_sequence_length_distribution_plot.txt
│ │ ├── fastqc-status-check-heatmap.txt
│ │ ├── fastqc_top_overrepresented_sequences_table.txt
│ │ ├── multiqc_citations.txt
│ │ ├── multiqc_data.json
│ │ ├── multiqc_fastqc.txt
│ │ ├── multiqc_general_stats.txt
│ │ ├── multiqc.log
│ │ ├── multiqc_nextclade.txt
│ │ ├── multiqc_pangolin.txt
│ │ ├── multiqc_samtools_flagstat.txt
│ │ ├── multiqc_samtools_stats.txt
│ │ ├── multiqc_seqyclean.txt
│ │ ├── multiqc_software_versions.txt
│ │ ├── multiqc_sources.txt
│ │ ├── nextclade_run_table.txt
│ │ ├── pangolin_run_table.txt
│ │ ├── samtools_alignment_plot.txt
│ │ ├── samtools-flagstat-dp.txt
│ │ ├── samtools-stats-dp.txt
│ │ ├── seqyclean-discarded-reads-plot.txt
│ │ ├── seqyclean-read-annotation-plot.txt
│ │ └── seqyclean-summary-plot.txt
│ └── multiqc_report.html
├── nextclade
│ ├── combined.fasta
│ ├── nextclade.aligned.fasta
│ ├── nextclade.auspice.json
│ ├── nextclade.cds_translation.E.fasta
│ ├── nextclade.cds_translation.M.fasta
│ ├── nextclade.cds_translation.N.fasta
│ ├── nextclade.cds_translation.ORF1a.fasta
│ ├── nextclade.cds_translation.ORF1b.fasta
│ ├── nextclade.cds_translation.ORF3a.fasta
│ ├── nextclade.cds_translation.ORF6.fasta
│ ├── nextclade.cds_translation.ORF7a.fasta
│ ├── nextclade.cds_translation.ORF7b.fasta
│ ├── nextclade.cds_translation.ORF8.fasta
│ ├── nextclade.cds_translation.ORF9b.fasta
│ ├── nextclade.cds_translation.S.fasta
│ ├── nextclade.csv
│ ├── nextclade.gff
│ ├── nextclade.json
│ ├── nextclade.ndjson
│ ├── nextclade.nwk
│ ├── nextclade.tbl
│ └── nextclade.tsv
├── pango_aliasor
│ └── pango_aliasor.csv
├── pangolin
│ ├── combined.fasta
│ └── lineage_report.csv
├── phytreeviz
│ └── tree.png
├── pipeline_info
│ ├── execution_report_2025-06-24_10-25-21.html
│ ├── execution_report_2025-06-24_10-29-25.html
│ ├── execution_report_2025-06-24_10-50-33.html
│ ├── execution_report_2025-06-24_11-33-11.html
│ ├── execution_timeline_2025-06-24_10-25-21.html
│ ├── execution_timeline_2025-06-24_10-29-25.html
│ ├── execution_timeline_2025-06-24_10-50-33.html
│ ├── execution_timeline_2025-06-24_11-33-11.html
│ ├── execution_trace_2025-06-24_10-25-21.txt
│ ├── execution_trace_2025-06-24_10-29-25.txt
│ ├── execution_trace_2025-06-24_10-49-58.txt
│ ├── execution_trace_2025-06-24_10-50-33.txt
│ ├── execution_trace_2025-06-24_11-33-11.txt
│ ├── pipeline_dag_2025-06-24_10-25-21.html
│ ├── pipeline_dag_2025-06-24_10-29-25.html
│ ├── pipeline_dag_2025-06-24_10-50-33.html
│ └── pipeline_dag_2025-06-24_11-33-11.html
├── samtools
│ ├── ERR5181310_ampliconstats.txt
│ ├── ERR5181310.final.cov.hist
│ ├── ERR5181310.final.cov.txt
│ ├── ERR5181310.final.depth.txt
│ ├── ERR5181310.final.flagstat.txt
│ ├── ERR5181310.final.stats.txt
│ ├── ERR5181310.initial.cov.hist
│ ├── ERR5181310.initial.cov.txt
│ ├── ERR5181310.initial.depth.txt
│ ├── ERR5181310.initial.flagstat.txt
│ ├── ERR5181310.initial.stats.txt
│ ├── ERR5181360_ampliconstats.txt
│ ├── ERR5181360.final.cov.hist
│ ├── ERR5181360.final.cov.txt
│ ├── ERR5181360.final.depth.txt
│ ├── ERR5181360.final.flagstat.txt
│ ├── ERR5181360.final.stats.txt
│ ├── ERR5181360.initial.cov.hist
│ ├── ERR5181360.initial.cov.txt
│ ├── ERR5181360.initial.depth.txt
│ ├── ERR5181360.initial.flagstat.txt
│ ├── ERR5181360.initial.stats.txt
│ ├── ERR5405022_ampliconstats.txt
│ ├── ERR5405022.final.cov.hist
│ ├── ERR5405022.final.cov.txt
│ ├── ERR5405022.final.depth.txt
│ ├── ERR5405022.final.flagstat.txt
│ ├── ERR5405022.final.stats.txt
│ ├── ERR5405022.initial.cov.hist
│ ├── ERR5405022.initial.cov.txt
│ ├── ERR5405022.initial.depth.txt
│ ├── ERR5405022.initial.flagstat.txt
│ ├── ERR5405022.initial.stats.txt
│ ├── ERR5556343_ampliconstats.txt
│ ├── ERR5556343.final.cov.hist
│ ├── ERR5556343.final.cov.txt
│ ├── ERR5556343.final.depth.txt
│ ├── ERR5556343.final.flagstat.txt
│ ├── ERR5556343.final.stats.txt
│ ├── ERR5556343.initial.cov.hist
│ ├── ERR5556343.initial.cov.txt
│ ├── ERR5556343.initial.depth.txt
│ ├── ERR5556343.initial.flagstat.txt
│ ├── ERR5556343.initial.stats.txt
│ ├── ERR5691945_ampliconstats.txt
│ ├── ERR5691945.final.cov.hist
│ ├── ERR5691945.final.cov.txt
│ ├── ERR5691945.final.depth.txt
│ ├── ERR5691945.final.flagstat.txt
│ ├── ERR5691945.final.stats.txt
│ ├── ERR5691945.initial.cov.hist
│ ├── ERR5691945.initial.cov.txt
│ ├── ERR5691945.initial.depth.txt
│ ├── ERR5691945.initial.flagstat.txt
│ ├── ERR5691945.initial.stats.txt
│ ├── ERR5743043_ampliconstats.txt
│ ├── ERR5743043.final.cov.hist
│ ├── ERR5743043.final.cov.txt
│ ├── ERR5743043.final.depth.txt
│ ├── ERR5743043.final.flagstat.txt
│ ├── ERR5743043.final.stats.txt
│ ├── ERR5743043.initial.cov.hist
│ ├── ERR5743043.initial.cov.txt
│ ├── ERR5743043.initial.depth.txt
│ ├── ERR5743043.initial.flagstat.txt
│ ├── ERR5743043.initial.stats.txt
│ ├── ERR5743893_ampliconstats.txt
│ ├── ERR5743893.final.cov.hist
│ ├── ERR5743893.final.cov.txt
│ ├── ERR5743893.final.depth.txt
│ ├── ERR5743893.final.flagstat.txt
│ ├── ERR5743893.final.stats.txt
│ ├── ERR5743893.initial.cov.hist
│ ├── ERR5743893.initial.cov.txt
│ ├── ERR5743893.initial.depth.txt
│ ├── ERR5743893.initial.flagstat.txt
│ ├── ERR5743893.initial.stats.txt
│ ├── ERR5749609_ampliconstats.txt
│ ├── ERR5749609.final.cov.hist
│ ├── ERR5749609.final.cov.txt
│ ├── ERR5749609.final.depth.txt
│ ├── ERR5749609.final.flagstat.txt
│ ├── ERR5749609.final.stats.txt
│ ├── ERR5749609.initial.cov.hist
│ ├── ERR5749609.initial.cov.txt
│ ├── ERR5749609.initial.depth.txt
│ ├── ERR5749609.initial.flagstat.txt
│ ├── ERR5749609.initial.stats.txt
│ ├── ERR5771988_ampliconstats.txt
│ ├── ERR5771988.final.cov.hist
│ ├── ERR5771988.final.cov.txt
│ ├── ERR5771988.final.depth.txt
│ ├── ERR5771988.final.flagstat.txt
│ ├── ERR5771988.final.stats.txt
│ ├── ERR5771988.initial.cov.hist
│ ├── ERR5771988.initial.cov.txt
│ ├── ERR5771988.initial.depth.txt
│ ├── ERR5771988.initial.flagstat.txt
│ ├── ERR5771988.initial.stats.txt
│ ├── final_samtools_coverage_summary.tsv
│ ├── SRR13422799_ampliconstats.txt
│ ├── SRR13422799.final.cov.hist
│ ├── SRR13422799.final.cov.txt
│ ├── SRR13422799.final.depth.txt
│ ├── SRR13422799.final.flagstat.txt
│ ├── SRR13422799.final.stats.txt
│ ├── SRR13422799.initial.cov.hist
│ ├── SRR13422799.initial.cov.txt
│ ├── SRR13422799.initial.depth.txt
│ ├── SRR13422799.initial.flagstat.txt
│ ├── SRR13422799.initial.stats.txt
│ ├── SRR13422802_ampliconstats.txt
│ ├── SRR13422802.final.cov.hist
│ ├── SRR13422802.final.cov.txt
│ ├── SRR13422802.final.depth.txt
│ ├── SRR13422802.final.flagstat.txt
│ ├── SRR13422802.final.stats.txt
│ ├── SRR13422802.initial.cov.hist
│ ├── SRR13422802.initial.cov.txt
│ ├── SRR13422802.initial.depth.txt
│ ├── SRR13422802.initial.flagstat.txt
│ ├── SRR13422802.initial.stats.txt
│ ├── SRR13500958_ampliconstats.txt
│ ├── SRR13500958.final.cov.hist
│ ├── SRR13500958.final.cov.txt
│ ├── SRR13500958.final.depth.txt
│ ├── SRR13500958.final.flagstat.txt
│ ├── SRR13500958.final.stats.txt
│ ├── SRR13500958.initial.cov.hist
│ ├── SRR13500958.initial.cov.txt
│ ├── SRR13500958.initial.depth.txt
│ ├── SRR13500958.initial.flagstat.txt
│ ├── SRR13500958.initial.stats.txt
│ ├── SRR13511054_ampliconstats.txt
│ ├── SRR13511054.final.cov.hist
│ ├── SRR13511054.final.cov.txt
│ ├── SRR13511054.final.depth.txt
│ ├── SRR13511054.final.flagstat.txt
│ ├── SRR13511054.final.stats.txt
│ ├── SRR13511054.initial.cov.hist
│ ├── SRR13511054.initial.cov.txt
│ ├── SRR13511054.initial.depth.txt
│ ├── SRR13511054.initial.flagstat.txt
│ ├── SRR13511054.initial.stats.txt
│ ├── SRR13603869_ampliconstats.txt
│ ├── SRR13603869.final.cov.hist
│ ├── SRR13603869.final.cov.txt
│ ├── SRR13603869.final.depth.txt
│ ├── SRR13603869.final.flagstat.txt
│ ├── SRR13603869.final.stats.txt
│ ├── SRR13603869.initial.cov.hist
│ ├── SRR13603869.initial.cov.txt
│ ├── SRR13603869.initial.depth.txt
│ ├── SRR13603869.initial.flagstat.txt
│ ├── SRR13603869.initial.stats.txt
│ ├── SRR13606410_ampliconstats.txt
│ ├── SRR13606410.final.cov.hist
│ ├── SRR13606410.final.cov.txt
│ ├── SRR13606410.final.depth.txt
│ ├── SRR13606410.final.flagstat.txt
│ ├── SRR13606410.final.stats.txt
│ ├── SRR13606410.initial.cov.hist
│ ├── SRR13606410.initial.cov.txt
│ ├── SRR13606410.initial.depth.txt
│ ├── SRR13606410.initial.flagstat.txt
│ ├── SRR13606410.initial.stats.txt
│ ├── SRR14241199_ampliconstats.txt
│ ├── SRR14241199.final.cov.hist
│ ├── SRR14241199.final.cov.txt
│ ├── SRR14241199.final.depth.txt
│ ├── SRR14241199.final.flagstat.txt
│ ├── SRR14241199.final.stats.txt
│ ├── SRR14241199.initial.cov.hist
│ ├── SRR14241199.initial.cov.txt
│ ├── SRR14241199.initial.depth.txt
│ ├── SRR14241199.initial.flagstat.txt
│ └── SRR14241199.initial.stats.txt
├── samtools_plot_ampliconstats
│ ├── ERR5181310
│ ├── ERR5181310-combined-amp.gp
│ ├── ERR5181310-combined-amp.png
│ ├── ERR5181310-combined-coverage-1.gp
│ ├── ERR5181310-combined-coverage-1.png
│ ├── ERR5181310-combined-depth.gp
│ ├── ERR5181310-combined-depth.png
│ ├── ERR5181310-combined-read-perc.gp
│ ├── ERR5181310-combined-read-perc.png
│ ├── ERR5181310-combined-reads.gp
│ ├── ERR5181310-combined-reads.png
│ ├── ERR5181310-combined-tcoord.gp
│ ├── ERR5181310-combined-tcoord.png
│ ├── ERR5181310-combined-tdepth.gp
│ ├── ERR5181310-combined-tdepth.png
│ ├── ERR5181310-ERR5181310.primertrim.sorted-amp.gp
│ ├── ERR5181310-ERR5181310.primertrim.sorted-amp.png
│ ├── ERR5181310-ERR5181310.primertrim.sorted-cov.gp
│ ├── ERR5181310-ERR5181310.primertrim.sorted-cov.png
│ ├── ERR5181310-ERR5181310.primertrim.sorted-reads.gp
│ ├── ERR5181310-ERR5181310.primertrim.sorted-reads.png
│ ├── ERR5181310-ERR5181310.primertrim.sorted-tcoord.gp
│ ├── ERR5181310-ERR5181310.primertrim.sorted-tcoord.png
│ ├── ERR5181310-ERR5181310.primertrim.sorted-tdepth.gp
│ ├── ERR5181310-ERR5181310.primertrim.sorted-tdepth.png
│ ├── ERR5181310-ERR5181310.primertrim.sorted-tsize.gp
│ ├── ERR5181310-ERR5181310.primertrim.sorted-tsize.png
│ ├── ERR5181310-heat-amp-1.gp
│ ├── ERR5181310-heat-amp-1.png
│ ├── ERR5181310-heat-coverage-1-1.gp
│ ├── ERR5181310-heat-coverage-1-1.png
│ ├── ERR5181310-heat-read-perc-1.gp
│ ├── ERR5181310-heat-read-perc-1.png
│ ├── ERR5181310-heat-read-perc-log-1.gp
│ ├── ERR5181310-heat-read-perc-log-1.png
│ ├── ERR5181310-heat-reads-1.gp
│ ├── ERR5181310-heat-reads-1.png
│ ├── ERR5181360
│ ├── ERR5181360-combined-amp.gp
│ ├── ERR5181360-combined-amp.png
│ ├── ERR5181360-combined-coverage-1.gp
│ ├── ERR5181360-combined-coverage-1.png
│ ├── ERR5181360-combined-depth.gp
│ ├── ERR5181360-combined-depth.png
│ ├── ERR5181360-combined-read-perc.gp
│ ├── ERR5181360-combined-read-perc.png
│ ├── ERR5181360-combined-reads.gp
│ ├── ERR5181360-combined-reads.png
│ ├── ERR5181360-combined-tcoord.gp
│ ├── ERR5181360-combined-tcoord.png
│ ├── ERR5181360-combined-tdepth.gp
│ ├── ERR5181360-combined-tdepth.png
│ ├── ERR5181360-ERR5181360.primertrim.sorted-amp.gp
│ ├── ERR5181360-ERR5181360.primertrim.sorted-amp.png
│ ├── ERR5181360-ERR5181360.primertrim.sorted-cov.gp
│ ├── ERR5181360-ERR5181360.primertrim.sorted-cov.png
│ ├── ERR5181360-ERR5181360.primertrim.sorted-reads.gp
│ ├── ERR5181360-ERR5181360.primertrim.sorted-reads.png
│ ├── ERR5181360-ERR5181360.primertrim.sorted-tcoord.gp
│ ├── ERR5181360-ERR5181360.primertrim.sorted-tcoord.png
│ ├── ERR5181360-ERR5181360.primertrim.sorted-tdepth.gp
│ ├── ERR5181360-ERR5181360.primertrim.sorted-tdepth.png
│ ├── ERR5181360-ERR5181360.primertrim.sorted-tsize.gp
│ ├── ERR5181360-ERR5181360.primertrim.sorted-tsize.png
│ ├── ERR5181360-heat-amp-1.gp
│ ├── ERR5181360-heat-amp-1.png
│ ├── ERR5181360-heat-coverage-1-1.gp
│ ├── ERR5181360-heat-coverage-1-1.png
│ ├── ERR5181360-heat-read-perc-1.gp
│ ├── ERR5181360-heat-read-perc-1.png
│ ├── ERR5181360-heat-read-perc-log-1.gp
│ ├── ERR5181360-heat-read-perc-log-1.png
│ ├── ERR5181360-heat-reads-1.gp
│ ├── ERR5181360-heat-reads-1.png
│ ├── ERR5405022
│ ├── ERR5405022-combined-amp.gp
│ ├── ERR5405022-combined-amp.png
│ ├── ERR5405022-combined-coverage-1.gp
│ ├── ERR5405022-combined-coverage-1.png
│ ├── ERR5405022-combined-depth.gp
│ ├── ERR5405022-combined-depth.png
│ ├── ERR5405022-combined-read-perc.gp
│ ├── ERR5405022-combined-read-perc.png
│ ├── ERR5405022-combined-reads.gp
│ ├── ERR5405022-combined-reads.png
│ ├── ERR5405022-combined-tcoord.gp
│ ├── ERR5405022-combined-tcoord.png
│ ├── ERR5405022-combined-tdepth.gp
│ ├── ERR5405022-combined-tdepth.png
│ ├── ERR5405022-ERR5405022.primertrim.sorted-amp.gp
│ ├── ERR5405022-ERR5405022.primertrim.sorted-amp.png
│ ├── ERR5405022-ERR5405022.primertrim.sorted-cov.gp
│ ├── ERR5405022-ERR5405022.primertrim.sorted-cov.png
│ ├── ERR5405022-ERR5405022.primertrim.sorted-reads.gp
│ ├── ERR5405022-ERR5405022.primertrim.sorted-reads.png
│ ├── ERR5405022-ERR5405022.primertrim.sorted-tcoord.gp
│ ├── ERR5405022-ERR5405022.primertrim.sorted-tcoord.png
│ ├── ERR5405022-ERR5405022.primertrim.sorted-tdepth.gp
│ ├── ERR5405022-ERR5405022.primertrim.sorted-tdepth.png
│ ├── ERR5405022-ERR5405022.primertrim.sorted-tsize.gp
│ ├── ERR5405022-ERR5405022.primertrim.sorted-tsize.png
│ ├── ERR5405022-heat-amp-1.gp
│ ├── ERR5405022-heat-amp-1.png
│ ├── ERR5405022-heat-coverage-1-1.gp
│ ├── ERR5405022-heat-coverage-1-1.png
│ ├── ERR5405022-heat-read-perc-1.gp
│ ├── ERR5405022-heat-read-perc-1.png
│ ├── ERR5405022-heat-read-perc-log-1.gp
│ ├── ERR5405022-heat-read-perc-log-1.png
│ ├── ERR5405022-heat-reads-1.gp
│ ├── ERR5405022-heat-reads-1.png
│ ├── ERR5556343
│ ├── ERR5556343-combined-amp.gp
│ ├── ERR5556343-combined-amp.png
│ ├── ERR5556343-combined-coverage-1.gp
│ ├── ERR5556343-combined-coverage-1.png
│ ├── ERR5556343-combined-depth.gp
│ ├── ERR5556343-combined-depth.png
│ ├── ERR5556343-combined-read-perc.gp
│ ├── ERR5556343-combined-read-perc.png
│ ├── ERR5556343-combined-reads.gp
│ ├── ERR5556343-combined-reads.png
│ ├── ERR5556343-combined-tcoord.gp
│ ├── ERR5556343-combined-tcoord.png
│ ├── ERR5556343-combined-tdepth.gp
│ ├── ERR5556343-combined-tdepth.png
│ ├── ERR5556343-ERR5556343.primertrim.sorted-amp.gp
│ ├── ERR5556343-ERR5556343.primertrim.sorted-amp.png
│ ├── ERR5556343-ERR5556343.primertrim.sorted-cov.gp
│ ├── ERR5556343-ERR5556343.primertrim.sorted-cov.png
│ ├── ERR5556343-ERR5556343.primertrim.sorted-reads.gp
│ ├── ERR5556343-ERR5556343.primertrim.sorted-reads.png
│ ├── ERR5556343-ERR5556343.primertrim.sorted-tcoord.gp
│ ├── ERR5556343-ERR5556343.primertrim.sorted-tcoord.png
│ ├── ERR5556343-ERR5556343.primertrim.sorted-tdepth.gp
│ ├── ERR5556343-ERR5556343.primertrim.sorted-tdepth.png
│ ├── ERR5556343-ERR5556343.primertrim.sorted-tsize.gp
│ ├── ERR5556343-ERR5556343.primertrim.sorted-tsize.png
│ ├── ERR5556343-heat-amp-1.gp
│ ├── ERR5556343-heat-amp-1.png
│ ├── ERR5556343-heat-coverage-1-1.gp
│ ├── ERR5556343-heat-coverage-1-1.png
│ ├── ERR5556343-heat-read-perc-1.gp
│ ├── ERR5556343-heat-read-perc-1.png
│ ├── ERR5556343-heat-read-perc-log-1.gp
│ ├── ERR5556343-heat-read-perc-log-1.png
│ ├── ERR5556343-heat-reads-1.gp
│ ├── ERR5556343-heat-reads-1.png
│ ├── ERR5691945
│ ├── ERR5691945-combined-amp.gp
│ ├── ERR5691945-combined-amp.png
│ ├── ERR5691945-combined-coverage-1.gp
│ ├── ERR5691945-combined-coverage-1.png
│ ├── ERR5691945-combined-depth.gp
│ ├── ERR5691945-combined-depth.png
│ ├── ERR5691945-combined-read-perc.gp
│ ├── ERR5691945-combined-read-perc.png
│ ├── ERR5691945-combined-reads.gp
│ ├── ERR5691945-combined-reads.png
│ ├── ERR5691945-combined-tcoord.gp
│ ├── ERR5691945-combined-tcoord.png
│ ├── ERR5691945-combined-tdepth.gp
│ ├── ERR5691945-combined-tdepth.png
│ ├── ERR5691945-ERR5691945.primertrim.sorted-amp.gp
│ ├── ERR5691945-ERR5691945.primertrim.sorted-amp.png
│ ├── ERR5691945-ERR5691945.primertrim.sorted-cov.gp
│ ├── ERR5691945-ERR5691945.primertrim.sorted-cov.png
│ ├── ERR5691945-ERR5691945.primertrim.sorted-reads.gp
│ ├── ERR5691945-ERR5691945.primertrim.sorted-reads.png
│ ├── ERR5691945-ERR5691945.primertrim.sorted-tcoord.gp
│ ├── ERR5691945-ERR5691945.primertrim.sorted-tcoord.png
│ ├── ERR5691945-ERR5691945.primertrim.sorted-tdepth.gp
│ ├── ERR5691945-ERR5691945.primertrim.sorted-tdepth.png
│ ├── ERR5691945-ERR5691945.primertrim.sorted-tsize.gp
│ ├── ERR5691945-ERR5691945.primertrim.sorted-tsize.png
│ ├── ERR5691945-heat-amp-1.gp
│ ├── ERR5691945-heat-amp-1.png
│ ├── ERR5691945-heat-coverage-1-1.gp
│ ├── ERR5691945-heat-coverage-1-1.png
│ ├── ERR5691945-heat-read-perc-1.gp
│ ├── ERR5691945-heat-read-perc-1.png
│ ├── ERR5691945-heat-read-perc-log-1.gp
│ ├── ERR5691945-heat-read-perc-log-1.png
│ ├── ERR5691945-heat-reads-1.gp
│ ├── ERR5691945-heat-reads-1.png
│ ├── ERR5743043
│ ├── ERR5743043-combined-amp.gp
│ ├── ERR5743043-combined-amp.png
│ ├── ERR5743043-combined-coverage-1.gp
│ ├── ERR5743043-combined-coverage-1.png
│ ├── ERR5743043-combined-depth.gp
│ ├── ERR5743043-combined-depth.png
│ ├── ERR5743043-combined-read-perc.gp
│ ├── ERR5743043-combined-read-perc.png
│ ├── ERR5743043-combined-reads.gp
│ ├── ERR5743043-combined-reads.png
│ ├── ERR5743043-combined-tcoord.gp
│ ├── ERR5743043-combined-tcoord.png
│ ├── ERR5743043-combined-tdepth.gp
│ ├── ERR5743043-combined-tdepth.png
│ ├── ERR5743043-ERR5743043.primertrim.sorted-amp.gp
│ ├── ERR5743043-ERR5743043.primertrim.sorted-amp.png
│ ├── ERR5743043-ERR5743043.primertrim.sorted-cov.gp
│ ├── ERR5743043-ERR5743043.primertrim.sorted-cov.png
│ ├── ERR5743043-ERR5743043.primertrim.sorted-reads.gp
│ ├── ERR5743043-ERR5743043.primertrim.sorted-reads.png
│ ├── ERR5743043-ERR5743043.primertrim.sorted-tcoord.gp
│ ├── ERR5743043-ERR5743043.primertrim.sorted-tcoord.png
│ ├── ERR5743043-ERR5743043.primertrim.sorted-tdepth.gp
│ ├── ERR5743043-ERR5743043.primertrim.sorted-tdepth.png
│ ├── ERR5743043-ERR5743043.primertrim.sorted-tsize.gp
│ ├── ERR5743043-ERR5743043.primertrim.sorted-tsize.png
│ ├── ERR5743043-heat-amp-1.gp
│ ├── ERR5743043-heat-amp-1.png
│ ├── ERR5743043-heat-coverage-1-1.gp
│ ├── ERR5743043-heat-coverage-1-1.png
│ ├── ERR5743043-heat-read-perc-1.gp
│ ├── ERR5743043-heat-read-perc-1.png
│ ├── ERR5743043-heat-read-perc-log-1.gp
│ ├── ERR5743043-heat-read-perc-log-1.png
│ ├── ERR5743043-heat-reads-1.gp
│ ├── ERR5743043-heat-reads-1.png
│ ├── ERR5743893
│ ├── ERR5743893-combined-amp.gp
│ ├── ERR5743893-combined-amp.png
│ ├── ERR5743893-combined-coverage-1.gp
│ ├── ERR5743893-combined-coverage-1.png
│ ├── ERR5743893-combined-depth.gp
│ ├── ERR5743893-combined-depth.png
│ ├── ERR5743893-combined-read-perc.gp
│ ├── ERR5743893-combined-read-perc.png
│ ├── ERR5743893-combined-reads.gp
│ ├── ERR5743893-combined-reads.png
│ ├── ERR5743893-combined-tcoord.gp
│ ├── ERR5743893-combined-tcoord.png
│ ├── ERR5743893-combined-tdepth.gp
│ ├── ERR5743893-combined-tdepth.png
│ ├── ERR5743893-ERR5743893.primertrim.sorted-amp.gp
│ ├── ERR5743893-ERR5743893.primertrim.sorted-amp.png
│ ├── ERR5743893-ERR5743893.primertrim.sorted-cov.gp
│ ├── ERR5743893-ERR5743893.primertrim.sorted-cov.png
│ ├── ERR5743893-ERR5743893.primertrim.sorted-reads.gp
│ ├── ERR5743893-ERR5743893.primertrim.sorted-reads.png
│ ├── ERR5743893-ERR5743893.primertrim.sorted-tcoord.gp
│ ├── ERR5743893-ERR5743893.primertrim.sorted-tcoord.png
│ ├── ERR5743893-ERR5743893.primertrim.sorted-tdepth.gp
│ ├── ERR5743893-ERR5743893.primertrim.sorted-tdepth.png
│ ├── ERR5743893-ERR5743893.primertrim.sorted-tsize.gp
│ ├── ERR5743893-ERR5743893.primertrim.sorted-tsize.png
│ ├── ERR5743893-heat-amp-1.gp
│ ├── ERR5743893-heat-amp-1.png
│ ├── ERR5743893-heat-coverage-1-1.gp
│ ├── ERR5743893-heat-coverage-1-1.png
│ ├── ERR5743893-heat-read-perc-1.gp
│ ├── ERR5743893-heat-read-perc-1.png
│ ├── ERR5743893-heat-read-perc-log-1.gp
│ ├── ERR5743893-heat-read-perc-log-1.png
│ ├── ERR5743893-heat-reads-1.gp
│ ├── ERR5743893-heat-reads-1.png
│ ├── ERR5749609
│ ├── ERR5749609-combined-amp.gp
│ ├── ERR5749609-combined-amp.png
│ ├── ERR5749609-combined-coverage-1.gp
│ ├── ERR5749609-combined-coverage-1.png
│ ├── ERR5749609-combined-depth.gp
│ ├── ERR5749609-combined-depth.png
│ ├── ERR5749609-combined-read-perc.gp
│ ├── ERR5749609-combined-read-perc.png
│ ├── ERR5749609-combined-reads.gp
│ ├── ERR5749609-combined-reads.png
│ ├── ERR5749609-combined-tcoord.gp
│ ├── ERR5749609-combined-tcoord.png
│ ├── ERR5749609-combined-tdepth.gp
│ ├── ERR5749609-combined-tdepth.png
│ ├── ERR5749609-ERR5749609.primertrim.sorted-amp.gp
│ ├── ERR5749609-ERR5749609.primertrim.sorted-amp.png
│ ├── ERR5749609-ERR5749609.primertrim.sorted-cov.gp
│ ├── ERR5749609-ERR5749609.primertrim.sorted-cov.png
│ ├── ERR5749609-ERR5749609.primertrim.sorted-reads.gp
│ ├── ERR5749609-ERR5749609.primertrim.sorted-reads.png
│ ├── ERR5749609-ERR5749609.primertrim.sorted-tcoord.gp
│ ├── ERR5749609-ERR5749609.primertrim.sorted-tcoord.png
│ ├── ERR5749609-ERR5749609.primertrim.sorted-tdepth.gp
│ ├── ERR5749609-ERR5749609.primertrim.sorted-tdepth.png
│ ├── ERR5749609-ERR5749609.primertrim.sorted-tsize.gp
│ ├── ERR5749609-ERR5749609.primertrim.sorted-tsize.png
│ ├── ERR5749609-heat-amp-1.gp
│ ├── ERR5749609-heat-amp-1.png
│ ├── ERR5749609-heat-coverage-1-1.gp
│ ├── ERR5749609-heat-coverage-1-1.png
│ ├── ERR5749609-heat-read-perc-1.gp
│ ├── ERR5749609-heat-read-perc-1.png
│ ├── ERR5749609-heat-read-perc-log-1.gp
│ ├── ERR5749609-heat-read-perc-log-1.png
│ ├── ERR5749609-heat-reads-1.gp
│ ├── ERR5749609-heat-reads-1.png
│ ├── ERR5771988
│ ├── ERR5771988-combined-amp.gp
│ ├── ERR5771988-combined-amp.png
│ ├── ERR5771988-combined-coverage-1.gp
│ ├── ERR5771988-combined-coverage-1.png
│ ├── ERR5771988-combined-depth.gp
│ ├── ERR5771988-combined-depth.png
│ ├── ERR5771988-combined-read-perc.gp
│ ├── ERR5771988-combined-read-perc.png
│ ├── ERR5771988-combined-reads.gp
│ ├── ERR5771988-combined-reads.png
│ ├── ERR5771988-combined-tcoord.gp
│ ├── ERR5771988-combined-tcoord.png
│ ├── ERR5771988-combined-tdepth.gp
│ ├── ERR5771988-combined-tdepth.png
│ ├── ERR5771988-ERR5771988.primertrim.sorted-amp.gp
│ ├── ERR5771988-ERR5771988.primertrim.sorted-amp.png
│ ├── ERR5771988-ERR5771988.primertrim.sorted-cov.gp
│ ├── ERR5771988-ERR5771988.primertrim.sorted-cov.png
│ ├── ERR5771988-ERR5771988.primertrim.sorted-reads.gp
│ ├── ERR5771988-ERR5771988.primertrim.sorted-reads.png
│ ├── ERR5771988-ERR5771988.primertrim.sorted-tcoord.gp
│ ├── ERR5771988-ERR5771988.primertrim.sorted-tcoord.png
│ ├── ERR5771988-ERR5771988.primertrim.sorted-tdepth.gp
│ ├── ERR5771988-ERR5771988.primertrim.sorted-tdepth.png
│ ├── ERR5771988-ERR5771988.primertrim.sorted-tsize.gp
│ ├── ERR5771988-ERR5771988.primertrim.sorted-tsize.png
│ ├── ERR5771988-heat-amp-1.gp
│ ├── ERR5771988-heat-amp-1.png
│ ├── ERR5771988-heat-coverage-1-1.gp
│ ├── ERR5771988-heat-coverage-1-1.png
│ ├── ERR5771988-heat-read-perc-1.gp
│ ├── ERR5771988-heat-read-perc-1.png
│ ├── ERR5771988-heat-read-perc-log-1.gp
│ ├── ERR5771988-heat-read-perc-log-1.png
│ ├── ERR5771988-heat-reads-1.gp
│ ├── ERR5771988-heat-reads-1.png
│ ├── index.html
│ ├── SRR13422799
│ ├── SRR13422799-combined-amp.gp
│ ├── SRR13422799-combined-amp.png
│ ├── SRR13422799-combined-coverage-1.gp
│ ├── SRR13422799-combined-coverage-1.png
│ ├── SRR13422799-combined-depth.gp
│ ├── SRR13422799-combined-depth.png
│ ├── SRR13422799-combined-read-perc.gp
│ ├── SRR13422799-combined-read-perc.png
│ ├── SRR13422799-combined-reads.gp
│ ├── SRR13422799-combined-reads.png
│ ├── SRR13422799-combined-tcoord.gp
│ ├── SRR13422799-combined-tcoord.png
│ ├── SRR13422799-combined-tdepth.gp
│ ├── SRR13422799-combined-tdepth.png
│ ├── SRR13422799-heat-amp-1.gp
│ ├── SRR13422799-heat-amp-1.png
│ ├── SRR13422799-heat-coverage-1-1.gp
│ ├── SRR13422799-heat-coverage-1-1.png
│ ├── SRR13422799-heat-read-perc-1.gp
│ ├── SRR13422799-heat-read-perc-1.png
│ ├── SRR13422799-heat-read-perc-log-1.gp
│ ├── SRR13422799-heat-read-perc-log-1.png
│ ├── SRR13422799-heat-reads-1.gp
│ ├── SRR13422799-heat-reads-1.png
│ ├── SRR13422799-SRR13422799.primertrim.sorted-amp.gp
│ ├── SRR13422799-SRR13422799.primertrim.sorted-amp.png
│ ├── SRR13422799-SRR13422799.primertrim.sorted-cov.gp
│ ├── SRR13422799-SRR13422799.primertrim.sorted-cov.png
│ ├── SRR13422799-SRR13422799.primertrim.sorted-reads.gp
│ ├── SRR13422799-SRR13422799.primertrim.sorted-reads.png
│ ├── SRR13422799-SRR13422799.primertrim.sorted-tcoord.gp
│ ├── SRR13422799-SRR13422799.primertrim.sorted-tcoord.png
│ ├── SRR13422799-SRR13422799.primertrim.sorted-tdepth.gp
│ ├── SRR13422799-SRR13422799.primertrim.sorted-tdepth.png
│ ├── SRR13422799-SRR13422799.primertrim.sorted-tsize.gp
│ ├── SRR13422799-SRR13422799.primertrim.sorted-tsize.png
│ ├── SRR13422802
│ ├── SRR13422802-combined-amp.gp
│ ├── SRR13422802-combined-amp.png
│ ├── SRR13422802-combined-coverage-1.gp
│ ├── SRR13422802-combined-coverage-1.png
│ ├── SRR13422802-combined-depth.gp
│ ├── SRR13422802-combined-depth.png
│ ├── SRR13422802-combined-read-perc.gp
│ ├── SRR13422802-combined-read-perc.png
│ ├── SRR13422802-combined-reads.gp
│ ├── SRR13422802-combined-reads.png
│ ├── SRR13422802-combined-tcoord.gp
│ ├── SRR13422802-combined-tcoord.png
│ ├── SRR13422802-combined-tdepth.gp
│ ├── SRR13422802-combined-tdepth.png
│ ├── SRR13422802-heat-amp-1.gp
│ ├── SRR13422802-heat-amp-1.png
│ ├── SRR13422802-heat-coverage-1-1.gp
│ ├── SRR13422802-heat-coverage-1-1.png
│ ├── SRR13422802-heat-read-perc-1.gp
│ ├── SRR13422802-heat-read-perc-1.png
│ ├── SRR13422802-heat-read-perc-log-1.gp
│ ├── SRR13422802-heat-read-perc-log-1.png
│ ├── SRR13422802-heat-reads-1.gp
│ ├── SRR13422802-heat-reads-1.png
│ ├── SRR13422802-SRR13422802.primertrim.sorted-amp.gp
│ ├── SRR13422802-SRR13422802.primertrim.sorted-amp.png
│ ├── SRR13422802-SRR13422802.primertrim.sorted-cov.gp
│ ├── SRR13422802-SRR13422802.primertrim.sorted-cov.png
│ ├── SRR13422802-SRR13422802.primertrim.sorted-reads.gp
│ ├── SRR13422802-SRR13422802.primertrim.sorted-reads.png
│ ├── SRR13422802-SRR13422802.primertrim.sorted-tcoord.gp
│ ├── SRR13422802-SRR13422802.primertrim.sorted-tcoord.png
│ ├── SRR13422802-SRR13422802.primertrim.sorted-tdepth.gp
│ ├── SRR13422802-SRR13422802.primertrim.sorted-tdepth.png
│ ├── SRR13422802-SRR13422802.primertrim.sorted-tsize.gp
│ ├── SRR13422802-SRR13422802.primertrim.sorted-tsize.png
│ ├── SRR13500958
│ ├── SRR13500958-combined-amp.gp
│ ├── SRR13500958-combined-amp.png
│ ├── SRR13500958-combined-coverage-1.gp
│ ├── SRR13500958-combined-coverage-1.png
│ ├── SRR13500958-combined-depth.gp
│ ├── SRR13500958-combined-depth.png
│ ├── SRR13500958-combined-read-perc.gp
│ ├── SRR13500958-combined-read-perc.png
│ ├── SRR13500958-combined-reads.gp
│ ├── SRR13500958-combined-reads.png
│ ├── SRR13500958-combined-tcoord.gp
│ ├── SRR13500958-combined-tcoord.png
│ ├── SRR13500958-combined-tdepth.gp
│ ├── SRR13500958-combined-tdepth.png
│ ├── SRR13500958-heat-amp-1.gp
│ ├── SRR13500958-heat-amp-1.png
│ ├── SRR13500958-heat-coverage-1-1.gp
│ ├── SRR13500958-heat-coverage-1-1.png
│ ├── SRR13500958-heat-read-perc-1.gp
│ ├── SRR13500958-heat-read-perc-1.png
│ ├── SRR13500958-heat-read-perc-log-1.gp
│ ├── SRR13500958-heat-read-perc-log-1.png
│ ├── SRR13500958-heat-reads-1.gp
│ ├── SRR13500958-heat-reads-1.png
│ ├── SRR13500958-SRR13500958.primertrim.sorted-amp.gp
│ ├── SRR13500958-SRR13500958.primertrim.sorted-amp.png
│ ├── SRR13500958-SRR13500958.primertrim.sorted-cov.gp
│ ├── SRR13500958-SRR13500958.primertrim.sorted-cov.png
│ ├── SRR13500958-SRR13500958.primertrim.sorted-reads.gp
│ ├── SRR13500958-SRR13500958.primertrim.sorted-reads.png
│ ├── SRR13500958-SRR13500958.primertrim.sorted-tcoord.gp
│ ├── SRR13500958-SRR13500958.primertrim.sorted-tcoord.png
│ ├── SRR13500958-SRR13500958.primertrim.sorted-tdepth.gp
│ ├── SRR13500958-SRR13500958.primertrim.sorted-tdepth.png
│ ├── SRR13500958-SRR13500958.primertrim.sorted-tsize.gp
│ ├── SRR13500958-SRR13500958.primertrim.sorted-tsize.png
│ ├── SRR13511054
│ ├── SRR13511054-combined-amp.gp
│ ├── SRR13511054-combined-amp.png
│ ├── SRR13511054-combined-coverage-1.gp
│ ├── SRR13511054-combined-coverage-1.png
│ ├── SRR13511054-combined-depth.gp
│ ├── SRR13511054-combined-depth.png
│ ├── SRR13511054-combined-read-perc.gp
│ ├── SRR13511054-combined-read-perc.png
│ ├── SRR13511054-combined-reads.gp
│ ├── SRR13511054-combined-reads.png
│ ├── SRR13511054-combined-tcoord.gp
│ ├── SRR13511054-combined-tcoord.png
│ ├── SRR13511054-combined-tdepth.gp
│ ├── SRR13511054-combined-tdepth.png
│ ├── SRR13511054-heat-amp-1.gp
│ ├── SRR13511054-heat-amp-1.png
│ ├── SRR13511054-heat-coverage-1-1.gp
│ ├── SRR13511054-heat-coverage-1-1.png
│ ├── SRR13511054-heat-read-perc-1.gp
│ ├── SRR13511054-heat-read-perc-1.png
│ ├── SRR13511054-heat-read-perc-log-1.gp
│ ├── SRR13511054-heat-read-perc-log-1.png
│ ├── SRR13511054-heat-reads-1.gp
│ ├── SRR13511054-heat-reads-1.png
│ ├── SRR13511054-SRR13511054.primertrim.sorted-amp.gp
│ ├── SRR13511054-SRR13511054.primertrim.sorted-amp.png
│ ├── SRR13511054-SRR13511054.primertrim.sorted-cov.gp
│ ├── SRR13511054-SRR13511054.primertrim.sorted-cov.png
│ ├── SRR13511054-SRR13511054.primertrim.sorted-reads.gp
│ ├── SRR13511054-SRR13511054.primertrim.sorted-reads.png
│ ├── SRR13511054-SRR13511054.primertrim.sorted-tcoord.gp
│ ├── SRR13511054-SRR13511054.primertrim.sorted-tcoord.png
│ ├── SRR13511054-SRR13511054.primertrim.sorted-tdepth.gp
│ ├── SRR13511054-SRR13511054.primertrim.sorted-tdepth.png
│ ├── SRR13511054-SRR13511054.primertrim.sorted-tsize.gp
│ ├── SRR13511054-SRR13511054.primertrim.sorted-tsize.png
│ ├── SRR13603869
│ ├── SRR13603869-combined-amp.gp
│ ├── SRR13603869-combined-amp.png
│ ├── SRR13603869-combined-coverage-1.gp
│ ├── SRR13603869-combined-coverage-1.png
│ ├── SRR13603869-combined-depth.gp
│ ├── SRR13603869-combined-depth.png
│ ├── SRR13603869-combined-read-perc.gp
│ ├── SRR13603869-combined-read-perc.png
│ ├── SRR13603869-combined-reads.gp
│ ├── SRR13603869-combined-reads.png
│ ├── SRR13603869-combined-tcoord.gp
│ ├── SRR13603869-combined-tcoord.png
│ ├── SRR13603869-combined-tdepth.gp
│ ├── SRR13603869-combined-tdepth.png
│ ├── SRR13603869-heat-amp-1.gp
│ ├── SRR13603869-heat-amp-1.png
│ ├── SRR13603869-heat-coverage-1-1.gp
│ ├── SRR13603869-heat-coverage-1-1.png
│ ├── SRR13603869-heat-read-perc-1.gp
│ ├── SRR13603869-heat-read-perc-1.png
│ ├── SRR13603869-heat-read-perc-log-1.gp
│ ├── SRR13603869-heat-read-perc-log-1.png
│ ├── SRR13603869-heat-reads-1.gp
│ ├── SRR13603869-heat-reads-1.png
│ ├── SRR13603869-SRR13603869.primertrim.sorted-amp.gp
│ ├── SRR13603869-SRR13603869.primertrim.sorted-amp.png
│ ├── SRR13603869-SRR13603869.primertrim.sorted-cov.gp
│ ├── SRR13603869-SRR13603869.primertrim.sorted-cov.png
│ ├── SRR13603869-SRR13603869.primertrim.sorted-reads.gp
│ ├── SRR13603869-SRR13603869.primertrim.sorted-reads.png
│ ├── SRR13603869-SRR13603869.primertrim.sorted-tcoord.gp
│ ├── SRR13603869-SRR13603869.primertrim.sorted-tcoord.png
│ ├── SRR13603869-SRR13603869.primertrim.sorted-tdepth.gp
│ ├── SRR13603869-SRR13603869.primertrim.sorted-tdepth.png
│ ├── SRR13603869-SRR13603869.primertrim.sorted-tsize.gp
│ ├── SRR13603869-SRR13603869.primertrim.sorted-tsize.png
│ ├── SRR13606410
│ ├── SRR13606410-combined-amp.gp
│ ├── SRR13606410-combined-amp.png
│ ├── SRR13606410-combined-coverage-1.gp
│ ├── SRR13606410-combined-coverage-1.png
│ ├── SRR13606410-combined-depth.gp
│ ├── SRR13606410-combined-depth.png
│ ├── SRR13606410-combined-read-perc.gp
│ ├── SRR13606410-combined-read-perc.png
│ ├── SRR13606410-combined-reads.gp
│ ├── SRR13606410-combined-reads.png
│ ├── SRR13606410-combined-tcoord.gp
│ ├── SRR13606410-combined-tcoord.png
│ ├── SRR13606410-combined-tdepth.gp
│ ├── SRR13606410-combined-tdepth.png
│ ├── SRR13606410-heat-amp-1.gp
│ ├── SRR13606410-heat-amp-1.png
│ ├── SRR13606410-heat-coverage-1-1.gp
│ ├── SRR13606410-heat-coverage-1-1.png
│ ├── SRR13606410-heat-read-perc-1.gp
│ ├── SRR13606410-heat-read-perc-1.png
│ ├── SRR13606410-heat-read-perc-log-1.gp
│ ├── SRR13606410-heat-read-perc-log-1.png
│ ├── SRR13606410-heat-reads-1.gp
│ ├── SRR13606410-heat-reads-1.png
│ ├── SRR13606410-SRR13606410.primertrim.sorted-amp.gp
│ ├── SRR13606410-SRR13606410.primertrim.sorted-amp.png
│ ├── SRR13606410-SRR13606410.primertrim.sorted-cov.gp
│ ├── SRR13606410-SRR13606410.primertrim.sorted-cov.png
│ ├── SRR13606410-SRR13606410.primertrim.sorted-reads.gp
│ ├── SRR13606410-SRR13606410.primertrim.sorted-reads.png
│ ├── SRR13606410-SRR13606410.primertrim.sorted-tcoord.gp
│ ├── SRR13606410-SRR13606410.primertrim.sorted-tcoord.png
│ ├── SRR13606410-SRR13606410.primertrim.sorted-tdepth.gp
│ ├── SRR13606410-SRR13606410.primertrim.sorted-tdepth.png
│ ├── SRR13606410-SRR13606410.primertrim.sorted-tsize.gp
│ ├── SRR13606410-SRR13606410.primertrim.sorted-tsize.png
│ ├── SRR14241199
│ ├── SRR14241199-combined-amp.gp
│ ├── SRR14241199-combined-amp.png
│ ├── SRR14241199-combined-coverage-1.gp
│ ├── SRR14241199-combined-coverage-1.png
│ ├── SRR14241199-combined-depth.gp
│ ├── SRR14241199-combined-depth.png
│ ├── SRR14241199-combined-read-perc.gp
│ ├── SRR14241199-combined-read-perc.png
│ ├── SRR14241199-combined-reads.gp
│ ├── SRR14241199-combined-reads.png
│ ├── SRR14241199-combined-tcoord.gp
│ ├── SRR14241199-combined-tcoord.png
│ ├── SRR14241199-combined-tdepth.gp
│ ├── SRR14241199-combined-tdepth.png
│ ├── SRR14241199-heat-amp-1.gp
│ ├── SRR14241199-heat-amp-1.png
│ ├── SRR14241199-heat-coverage-1-1.gp
│ ├── SRR14241199-heat-coverage-1-1.png
│ ├── SRR14241199-heat-read-perc-1.gp
│ ├── SRR14241199-heat-read-perc-1.png
│ ├── SRR14241199-heat-read-perc-log-1.gp
│ ├── SRR14241199-heat-read-perc-log-1.png
│ ├── SRR14241199-heat-reads-1.gp
│ ├── SRR14241199-heat-reads-1.png
│ ├── SRR14241199-SRR14241199.primertrim.sorted-amp.gp
│ ├── SRR14241199-SRR14241199.primertrim.sorted-amp.png
│ ├── SRR14241199-SRR14241199.primertrim.sorted-cov.gp
│ ├── SRR14241199-SRR14241199.primertrim.sorted-cov.png
│ ├── SRR14241199-SRR14241199.primertrim.sorted-reads.gp
│ ├── SRR14241199-SRR14241199.primertrim.sorted-reads.png
│ ├── SRR14241199-SRR14241199.primertrim.sorted-tcoord.gp
│ ├── SRR14241199-SRR14241199.primertrim.sorted-tcoord.png
│ ├── SRR14241199-SRR14241199.primertrim.sorted-tdepth.gp
│ ├── SRR14241199-SRR14241199.primertrim.sorted-tdepth.png
│ ├── SRR14241199-SRR14241199.primertrim.sorted-tsize.gp
│ └── SRR14241199-SRR14241199.primertrim.sorted-tsize.png
├── seqyclean
│ ├── Combined_SummaryStatistics.tsv
│ ├── ERR5181310_clean_PE1.fastq.gz
│ ├── ERR5181310_clean_PE2.fastq.gz
│ ├── ERR5181310_clean_SummaryStatistics.tsv
│ ├── ERR5181360_clean_PE1.fastq.gz
│ ├── ERR5181360_clean_PE2.fastq.gz
│ ├── ERR5181360_clean_SummaryStatistics.tsv
│ ├── ERR5405022_clean_PE1.fastq.gz
│ ├── ERR5405022_clean_PE2.fastq.gz
│ ├── ERR5405022_clean_SummaryStatistics.tsv
│ ├── ERR5556343_clean_PE1.fastq.gz
│ ├── ERR5556343_clean_PE2.fastq.gz
│ ├── ERR5556343_clean_SummaryStatistics.tsv
│ ├── ERR5691945_clean_PE1.fastq.gz
│ ├── ERR5691945_clean_PE2.fastq.gz
│ ├── ERR5691945_clean_SummaryStatistics.tsv
│ ├── ERR5743043_clean_PE1.fastq.gz
│ ├── ERR5743043_clean_PE2.fastq.gz
│ ├── ERR5743043_clean_SummaryStatistics.tsv
│ ├── ERR5743893_clean_PE1.fastq.gz
│ ├── ERR5743893_clean_PE2.fastq.gz
│ ├── ERR5743893_clean_SummaryStatistics.tsv
│ ├── ERR5749609_clean_PE1.fastq.gz
│ ├── ERR5749609_clean_PE2.fastq.gz
│ ├── ERR5749609_clean_SummaryStatistics.tsv
│ ├── ERR5771988_clean_PE1.fastq.gz
│ ├── ERR5771988_clean_PE2.fastq.gz
│ ├── ERR5771988_clean_SummaryStatistics.tsv
│ ├── SRR13422799_clean_PE1.fastq.gz
│ ├── SRR13422799_clean_PE2.fastq.gz
│ ├── SRR13422799_clean_SummaryStatistics.tsv
│ ├── SRR13422802_clean_PE1.fastq.gz
│ ├── SRR13422802_clean_PE2.fastq.gz
│ ├── SRR13422802_clean_SummaryStatistics.tsv
│ ├── SRR13500958_clean_PE1.fastq.gz
│ ├── SRR13500958_clean_PE2.fastq.gz
│ ├── SRR13500958_clean_SummaryStatistics.tsv
│ ├── SRR13511054_clean_PE1.fastq.gz
│ ├── SRR13511054_clean_PE2.fastq.gz
│ ├── SRR13511054_clean_SummaryStatistics.tsv
│ ├── SRR13603869_clean_PE1.fastq.gz
│ ├── SRR13603869_clean_PE2.fastq.gz
│ ├── SRR13603869_clean_SummaryStatistics.tsv
│ ├── SRR13606410_clean_PE1.fastq.gz
│ ├── SRR13606410_clean_PE2.fastq.gz
│ ├── SRR13606410_clean_SummaryStatistics.tsv
│ ├── SRR14241199_clean_PE1.fastq.gz
│ ├── SRR14241199_clean_PE2.fastq.gz
│ └── SRR14241199_clean_SummaryStatistics.tsv
├── snp-dists
│ └── snp-dists.txt
├── software_versions.yml
└── vadr
├── combined.fasta
├── trimmed.fasta
├── vadr.vadr.alc
├── vadr.vadr.alt
├── vadr.vadr.alt.list
├── vadr.vadr.cmd
├── vadr.vadr.dcr
├── vadr.vadr.fail.fa
├── vadr.vadr.fail.list
├── vadr.vadr.fail.tbl
├── vadr.vadr.filelist
├── vadr.vadr.ftr
├── vadr.vadr.log
├── vadr.vadr.mdl
├── vadr.vadr.pass.fa
├── vadr.vadr.pass.list
├── vadr.vadr.pass.tbl
├── vadr.vadr.rpn
├── vadr.vadr.sda
├── vadr.vadr.seqstat
├── vadr.vadr.sgm
├── vadr.vadr.sqa
└── vadr.vadr.sqc
There are two main files that summarize the information from this workflow. One is a csv file with the key result from each process, and one is the multiqc report. The default location for these files is cecret/cecret_results.csv and cecret/multiqc/multiqc_report.html. If using an alternative destination, set params.outdir to your preferred destination (see: instructions on how to adjust parameters).
There are summary files for each run found at cecret/cecret_results.csv and cecret/cecret_results.txt. These two files are exactly the same except for the delimiter used to separate the columns.
An example file run with the default values for some SARS-CoV-2 fastq files SRR13957125, SRR13957170, and SRR13957177 are below.
| sample_id | sample | pangolin_lineage | nextclade_clade | vadr_p/f | fasta_line | fastqc_raw_reads_1 | fastqc_raw_reads_2 | num_N | num_total | seqyclean_PairsKept | seqyclean_Perc_Kept | num_pos_100X | aci_num_failed_amplicons | insert_size_after_trimming | ivar_num_variants_identified | bcftools_variants_identified | samtools_meandepth_after_trimming | samtools_per_1X_coverage_after_trimming | vadr_model | vadr_alerts | nextclade_clade_who | nextclade_qc_overallscore | nextclade_qc_overallstatus | pangolin_conflict | pangolin_ambiguity_score | pangolin_scorpio_call | pangolin_scorpio_support | pangolin_scorpio_conflict | pangolin_scorpio_notes | pangolin_version | pangolin_pangolin_version | pangolin_scorpio_version | pangolin_constellation_version | pangolin_is_designated | pangolin_qc_status | pangolin_qc_notes | pangolin_note | pangocollapse_lineage | pangocollapse_Lineage_full | pangocollapse_Lineage_expanded | pangocollapse_Lineage_family | freyja_summarized | Cecret version | seqyclean | bwa | ivar | ivar consensus |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| SRR13957125 | SRR13957125 | B.1.429 | 21C | PASS | SRR13957125 | 670879.0 | 670879.0 | 667.0 | 29875.0 | 576244.0 | 85.8939 | 29200.0 | 2.0 | 199.0 | 27.0 | 27.0 | 5401.08 | 99.6522 | NC_045512 | - | Epsilon | 12.958697 | good | 0.0 | Epsilon (B.1.429-like) | 1.0 | 0.0 | scorpio call: Alt alleles 14; Ref alleles 0; Amb alleles 0; Oth alleles 0 | PUSHER-v1.23.1 | 4.3.1 | 0.3.19 | v0.1.12 | False | pass | Ambiguous content: 4% | Usher placements: B.1.429(1/1) | B.1.429 | B.1.429 | B.1.429 | B | [('Epsilon' 0.9990499999965543)] | v3.10.20231226 | seqyclean : Version: 1.10.09 (2018-10-16) | bwa : Version: 0.7.17-r1188 | ivar : iVar version 1.4.2 | iVar version 1.4.2 | |
| SRR13957170 | SRR13957170 | Unassigned | SRR13957170 | 2287.0 | 2287.0 | 25545.0 | 25545.0 | 176.0 | 7.69567 | 0.0 | 99.0 | 160.0 | 0.0 | 6.0 | 0.182791 | 6.91235 | PUSHER-v1.23.1 | 4.3.1 | 0.3.19 | v0.1.12 | False | fail | Failed to map | Unassigned | Unassigned | Unassigned | Unassigned | v3.10.20231226 | seqyclean : Version: 1.10.09 (2018-10-16) | bwa : Version: 0.7.17-r1188 | ivar : iVar version 1.4.2 | iVar version 1.4.2 | |||||||||||||||
| SRR13957177 | SRR13957177 | B.1.1.7 | 20I | PASS | SRR13957177 | 902426.0 | 902426.0 | 776.0 | 29787.0 | 837318.0 | 92.7852 | 29019.0 | 2.0 | 207.3 | 39.0 | 41.0 | 7621.74 | 99.8495 | NC_045512 | - | Alpha | 5.885816 | good | 0.0 | Alpha (B.1.1.7-like) | 0.96 | 0.04 | scorpio call: Alt alleles 22; Ref alleles 1; Amb alleles 0; Oth alleles 0 | PUSHER-v1.23.1 | 4.3.1 | 0.3.19 | v0.1.12 | False | pass | Ambiguous content: 4% | Usher placements: B.1.1.7(1/1) | B.1.1.7 | B.1.1.7 | B.1.1.7 | B.1.1.7 | [('Alpha' 0.999009112161133)] | v3.10.20231226 | seqyclean : Version: 1.10.09 (2018-10-16) | bwa : Version: 0.7.17-r1188 | ivar : iVar version 1.4.2 | iVar version 1.4.2 |
The multiqc report aggregates data across your samples into one file. Open the 'cecret/multiqc/multiqc_report.html' file with your favored browser. There tables and graphs are generated for 'General Statistics', 'Samtools stats', 'Samtools flagstats', 'FastQC', 'SeqyClean', 'Fastp', 'Pangolin', and 'Kraken2'. There are also added custom sections for many additional analysis including Freyja.
Nextflow will also produce files. These files are more about the resources that the system used than about analysis of the data. They are found in {params.outdir}/pipeline_info/.
If using Nextflow Tower or Seqera Platform, these are the files that appear in the reports section of the UI.
Currently, the summary file for the workflow (cecret_results.*) and the multiqc report (multiqc_report.html) are included. More may be added once UPHL gains access to this resource.
This is a report of the workflow that may be useful in determining computational resource use. This includes the command that was used, the directories and other storage locations that were used, and information about the processes being run.
Visually shows the timeline for each process given the computational environment.
A directory for all the temporary files used in the analysis. Users can generally delete this directory when the workflow is complete because 1) it generally is not needed if everything is run successfully and 2) because it is VERY large. Users will not be able to use nextflow -resume if this directory is deleted.
