4. Outputs - DOH-JDJ0303/bigbacter-nf GitHub Wiki
All Outputs
π¦${outdir}
β£ π${timestamp}
β β£ π${taxa}
β β β£ π${cluster}
β β β β£ πalns
β β β β£π${timestamp}-${taxa}-${cluster}.{gubbins,snippy}.aln
β β β β£ πdists
β β β β βπ${timestamp}-${taxa}-${cluster}-{accessory,core-snps}_.{poppunk,gubbins,snippy}-{long,wide}.csv
β β β β£ πfigures
β β β β β£π${timestamp}-${taxa}-${cluster}-core-snps_{ML,NJ}.{gubbins,snippy}.jpg
β β β β βπ${timestamp}-${taxa}-${cluster}-{accessory,core-snps}_dist.{poppunk,gubbins,snippy}.jpg
β β β β£ πsnippy
β β β β β π${timestamp}-${species}-${sample}.tar.gz
β β β β£ πstats
β β β β β π${timestamp}-${species}-${sample}.{gubbins,snippy}.stats
β β β β πtrees
β β β βπ${timestamp}-${taxa}-${cluster}-core-snps_{ML,NJ}.{gubbins,snippy}.nwk
β β β£ πpoppunk
β β β β£ π${timestamp}-${species}-pp_core_NJ.nwk
β β β β£ π${timestamp}-${species}-pp_microreact_clusters.csv
β β β β£ π${timestamp}-${species}-pp_perplexity20.0_accessory_mandrake.dot
β β β β£ π${timestamp}-${species}-pp.microreact
β β β β£ π${timestamp}-${species}-pp-core-acc-dist.txt.gz
β β β β£ π${timestamp}-${species}-pp-jaccard-dist.txt.gz
β β β β π${timestamp}-${species}-pp-clusters.csv
β β β£ πother
β β β β£ πmultiqc_report.html
β β β β πsoftware_versions.yml
β β β π${timestamp}-summary.tsv
β β π${timestamp}-db-info.csv
Results Summary
Results are summarized for all samples included in the analysis. This includes both new samples and those that were stored in your BigBacter database. Subsets of this summary are also saved for each species-cluster.
${timestamp}-summary.tsv
${timestamp}-${species}-${cluster}-summary.csv
PopPUNK Results (πpoppunk/)
PopPUNK Visualizations
These files are generated via poppunk_visualise
with the --microreact
option. You can view the .microreact
file at https://microreact.org/upload.
${timestamp}-${species}-pp_core_NJ.nwk
${timestamp}-${species}-pp_microreact_clusters.csv
${timestamp}-${species}-pp_perplexity20.0_accessory_mandrake.dot
${timestamp}-${species}-pp.microreact
All PopPUNK clusters
This contains clustering information for all samples in the PopPUNK database. It should contain the same information as ${timestamp}-${species}-pp_microreact_clusters.csv
.
${timestamp}-${species}-pp-clusters.csv
All PopPUNK distances
These are the pairwise core/accessory distances and Jaccard distances (same as Mash) produced from the PopPUNK database using sketchlib query
.
${timestamp}-${species}-pp-core-acc-dist.txt.gz
${timestamp}-${species}-pp-jaccard-dist.txt.gz
Alignment Files (πalns/)
Whole genome (snippy) or core genome (gubbins) alignment files.
${timestamp}-${taxa}-${cluster}.{gubbins,snippy}.aln
Pairwise Distances (πdists/)
Pairwise distance files in long and wide formats. Included for core SNPs (snippy & gubbins) and accessory distances.
${timestamp}-${taxa}-${cluster}-{accessory,core-snps}_.{poppunk,gubbins,snippy}-{long,wide}.csv
Figures (πfigures/)
Image files (.jpg) of pairwise distance matrices and/or phylogenetic trees. New samples are shown in bold, black text. Historic samples are shown in grey, plain text. Asterisks on nodes indicate bootstrap values < 70%.
π${timestamp}-${taxa}-${cluster}-core-snps\_{ML,NJ}.{gubbins,snippy}.jpg
π${timestamp}-${taxa}-${cluster}-{accessory,core-snps}\_dist.{poppunk,gubbins,snippy}.jpg
Individual Snippy Files (πsnippy/)
Tar files containing all the info needed to perform SNP analysis using snippy-core
.
${timestamp}-${species}-${sample}.tar.gz
Analysis Statistics (πstats/)
Sample statistics for snippy and gubbins.
${timestamp}-${species}-${sample}.{gubbins,snippy}.stats
Phylogenetic trees (πtrees/)
Maximum likelihood or neighbor joining trees generated from Snippy or Gubbins core SNP alignments.
${timestamp}-${taxa}-${cluster}-core-snps\_{ML,NJ}.{gubbins,snippy}.nwk \
Database Info
Snapshot of your BigBacter database. This is only generated if --db_info
is true
.
${timestamp}-db-info.csv \