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5. 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}-${cluster}-core-snps_{ML,NJ}.{gubbins,snippy}.microreact
┃ ┃ ┃ ┃ ┣📜${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
┃ ┃ ┣ 📂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
┃ ┃ ┗ 📜${timestamp}-summary.tsv
┃ ┗ 📜${timestamp}-db-info.csv
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
| Column Name | Description |
|---|---|
| ID | Sample ID (_T[0-9]+ denotes replicate number) |
| STATUS | Sample status (NEW or OLD) |
| QUAL | Sample quality status (PASS or 'FAIL'). Based on values in PER_GENFRAC, PER_HET, and PER_LOWCOV
|
| RUN_ID | Run timestamp |
| TAXA | Sample taxonomy (same as supplied in the samplesheet via taxa) |
| CLUSTER | Assigned PopPUNK cluster |
| ISO_IN_CLUSTER | Total number of isolates in the assigned PopPUNK cluster |
| ISO_PASS_QC | Number of isolates in the assigned PopPUNK cluster that passed QC |
| MEAN_SNP_DIST_SNIPPY | Mean pairwise SNP distances between the sample and all other isolates in the assigned cluster that passed QC, including the reference (without recombination masked) |
| MIN_SNP_DIST_SNIPPY | Minimum pairwise SNP distances between the sample and all other isolates in the assigned cluster that passed QC, including the reference (without recombination masked) |
| MAX_SNP_DIST_SNIPPY | Maximum pairwise SNP distances between the sample and all other isolates in the assigned cluster that passed QC, including the reference (without recombination masked) |
| STRONG_LINKAGE_SNIPPY | List of samples in the cluster with pairwise SNP differences <= --strong_link_cutoff (without recombination masked) |
| INTER_LINKAGE_SNIPPY | List of samples in the cluster with pairwise SNP differences between --strong_link_cutoff and --inter_link_cutoff (without recombination masked) |
| MEAN_SNP_DIST_GUBBINS | Mean pairwise SNP distances between the sample and all other isolates in the assigned cluster that passed QC, including the reference (with recombination masked) |
| MIN_SNP_DIST_GUBBINS | Minimum pairwise SNP distances between the sample and all other isolates in the assigned cluster that passed QC, including the reference (with recombination masked) |
| MAX_SNP_DIST_GUBBINS | Maximum pairwise SNP distances between the sample and all other isolates in the assigned cluster that passed QC, including the reference (with recombination masked) |
| STRONG_LINKAGE_GUBBINS | List of samples in the cluster with pairwise SNP differences <= --strong_link_cutoff (with recombination masked) |
| INTER_LINKAGE_GUBBINS | List of samples in the cluster with pairwise SNP differences between --strong_link_cutoff and --inter_link_cutoff (with recombination masked) |
| LENGTH | Length of the reference genome (bp) |
| ALIGNED | Reference positions covered by the sample (bp) |
| UNALIGNED | Reference positions not covered by the sample (bp) |
| RECOMB | Number of sites in recombinant regions, including variant and invariant sites (bp). |
| VARIANT | Number of variant sites detected in the sample, as compared to the reference (bp) |
| HET | Number of heterogenous sites (bp) |
| MASKED | Number of masked sites (bp) |
| LOWCOV | Number of low coverage sites (bp) |
| PER_GENFRAC | Percentage of the reference genome covered by the sample |
| PER_LOWCOV | |
| PER_HET | Percentage of the reference genome with heterogeneous sites |
Visualizations of the PopPUNK database 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
Cluster assignments for all samples in the PopPUNK database. Should contain the same information as ${timestamp}-${species}-pp_microreact_clusters.csv.
${timestamp}-${species}-pp-clusters.csv
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
Whole genome (snippy) or core genome (gubbins) alignment files.
${timestamp}-${taxa}-${cluster}.{gubbins,snippy}.aln
Pairwise distance files in long and wide formats. Included for core SNPs (snippy & gubbins) and accessory distances.
${timestamp}-${taxa}-${cluster}-{accessory,core-snps}_.{poppunk,gubbins,snippy}-{long,wide}.csv
Static image files (.jpg) and Microreact files of pairwise distance matrices and/or phylogenetic trees.
📜${timestamp}-${taxa}-${cluster}-core-snps\_{ML,NJ}.{gubbins,snippy}.jpg
📜${timestamp}-${taxa}-${cluster}-{accessory,core-snps}\_dist.{poppunk,gubbins,snippy}.jpg
Note
Static images: new samples are shown in bold, black text. Historic samples are shown in grey, plain text. Asterisks on nodes indicate bootstrap values < 70%.
Tar files containing all the info needed to perform SNP analysis using snippy-core.
${timestamp}-${species}-${sample}.tar.gz
Sample statistics for snippy and gubbins.
${timestamp}-${species}-${sample}.{gubbins,snippy}.stats
Maximum likelihood or neighbor joining trees generated from Snippy or Gubbins core SNP alignments.
${timestamp}-${taxa}-${cluster}-core-snps\_{ML,NJ}.{gubbins,snippy}.nwk \
Snapshot of your BigBacter database. This is only generated if --db_info is true.
${timestamp}-db-info.csv \