4. Outputs - DOH-JDJ0303/bigbacter-nf GitHub Wiki

All Outputs

📦${outdir}
┣ 📂${timestamp}
┃ ┣ 📂${taxa}
┃ ┃ ┣ 📂${cluster}
┃ ┃ ┃ ┣ 📂alns
┃ ┃ ┃ ┣📜${timestamp}-${taxa}-${cluster}.{gubbins,snippy}.aln
┃ ┃ ┃ ┣ 📂dists
┃ ┃ ┃ ┃ ┗📜${timestamp}-${taxa}-${cluster}-{accessory,core-snps}_.{poppunk,gubbins,snippy}-{long,wide}.csv
┃ ┃ ┃ ┣ 📂figures
┃ ┃ ┃ ┃ ┣📜${timestamp}-${taxa}-${cluster}-core-snps_{ML,NJ}.{gubbins,snippy}.jpg
┃ ┃ ┃ ┃ ┗📜${timestamp}-${taxa}-${cluster}-{accessory,core-snps}_dist.{poppunk,gubbins,snippy}.jpg
┃ ┃ ┃ ┣ 📂snippy
┃ ┃ ┃ ┃ ┗ 📜${timestamp}-${species}-${sample}.tar.gz
┃ ┃ ┃ ┣ 📂stats
┃ ┃ ┃ ┃ ┗ 📜${timestamp}-${species}-${sample}.{gubbins,snippy}.stats
┃ ┃ ┃ ┣ 📂trees
┃ ┃ ┃ ┃ ┗📜${timestamp}-${taxa}-${cluster}-core-snps_{ML,NJ}.{gubbins,snippy}.nwk
┃ ┃ ┃ ┗📜${timestamp}-${species}-db-info.txt
┃ ┃ ┣ 📂poppunk
┃ ┃ ┃ ┣ 📜${timestamp}-${species}-pp_core_NJ.nwk
┃ ┃ ┃ ┣ 📜${timestamp}-${species}-pp_microreact_clusters.csv
┃ ┃ ┃ ┣ 📜${timestamp}-${species}-pp_perplexity20.0_accessory_mandrake.dot
┃ ┃ ┃ ┣ 📜${timestamp}-${species}-pp.microreact
┃ ┃ ┃ ┣ 📜${timestamp}-${species}-pp-core-acc-dist.txt.gz
┃ ┃ ┃ ┣ 📜${timestamp}-${species}-pp-jaccard-dist.txt.gz
┃ ┃ ┃ ┗ 📜${timestamp}-${species}-pp-clusters.csv
┃ ┃ ┣ 📂other
┃ ┃ ┃ ┣ 📜multiqc_report.html
┃ ┃ ┃ ┗ 📜software_versions.yml
┃ ┃ ┗ 📜${timestamp}-summary.tsv \

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 (📂poppunk/)

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 (📂alns/)

Whole genome (snippy) or core genome (gubbins) alignment files.

${timestamp}-${taxa}-${cluster}.{gubbins,snippy}.aln

Pairwise Distances (📂dists/)

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 (📂figures/)

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%.

📜${timestamp}-${taxa}-${cluster}-core-snps\_{ML,NJ}.{gubbins,snippy}.jpg
📜${timestamp}-${taxa}-${cluster}-{accessory,core-snps}\_dist.{poppunk,gubbins,snippy}.jpg

Individual Snippy Files (📂snippy/)

Tar files containing all the info needed to perform SNP analysis using snippy-core.

${timestamp}-${species}-${sample}.tar.gz

Analysis Statistics (📂stats/)

Sample statistics for snippy and gubbins.

${timestamp}-${species}-${sample}.{gubbins,snippy}.stats

Phylogenetic trees (📂trees/)

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 all isolates in your species-specific BigBacter database and their corresponding cluster. This does not include samples on the current run.

${timestamp}-${species}-db-info.txt \