README.md

Below is a description of the files in this directory and subdirectories.

data Folder

└── data
    ├── bactopia-analysis.html
    ├── fastani
    │   └── crispatus-include.txt
    ├── gtdb
    │   ├── exclude.txt
    │   ├── gtdbtk.filtered.tsv
    │   └── gtdbtk.summary.tsv
    ├── lactobacillus-accessions.txt
    ├── lactobacillus-results.txt
    ├── lactobacillus-summary.txt
    ├── phyloflash
    │   ├── phyloflash-alignment.fasta.gz
    │   ├── phyloflash-contree.txt
    │   ├── phyloflash-iqtree.txt
    │   ├── phyloflash-merged.fasta.gz
    │   └── phyloflash-summary.txt
    ├── roary
    │   ├── core-genome.aligned.fa.gz
    │   ├── core-genome.contree
    │   ├── core-genome.distance.txt
    │   └── core-genome.iqtree
    └── summary
        ├── amrfinder
        │   ├── amrfinder-gene-detailed-summary.txt
        │   ├── amrfinder-gene-summary.txt
        │   ├── amrfinder-protein-detailed-summary.txt
        │   └── amrfinder-protein-summary.txt
        ├── ariba
        │   ├── ariba-card-detailed-summary.txt
        │   ├── ariba-card-summary.txt
        │   ├── ariba-vfdb_core-detailed-summary.txt
        │   └── ariba-vfdb_core-summary.txt
        ├── lactobacillus-exclude.txt
        ├── lactobacillus-report.txt
        └── lactobacillus-summary.txt

This directory contains the files used to create the final results and phylogenies.

Filename	Description
bactopia-analysis.html	HTML output created from the R Markdown script bactopia-analysis.Rmd in the scripts directory

Directories

fastani

Filename	Description
crispatus-include.txt	List of genomes with > 95% ANI to Lactobacillus crispatus

gtdb

Filename	Description
exclude.txt	Genomes not classified as Lactobacillus
gtdbtk.filtered.tsv	List of genomes with an insufficient number of amino acids in MSA
gtdbtk.summary.tsv	A summary of classifications provided by GTDB-Tk, see classification summary for more details

phyloflash

Filename	Description
phyloflash-alignment.fasta.gz	The multiple sequence alignment of 16S genes
phyloflash-contree.txt	Consensus tree with assigned branch supports created from 16S alignments
phyloflash-iqtree.txt	Full result of the run, this is the main report file
phyloflash-merged.fasta.gz	All 16S genes used in the multiple sequence alignment
phyloflash-summary.txt	The aggregated phyloFlash results of all samples

roary

The results of the Lactobacillus crispatus pan-genome

Filename	Description
core-genome.aligned.fa.gz	The multiple sequence alignment of core genes
core-genome.contree	Consensus tree with assigned branch supports created from 16S alignments
core-genome.distance.txt	Pairwise core genome SNP distance matrix
core-genome.iqtree	Full result of the IQTree run, this is the main report file

summary

Filename	Description
{amrfinder|ariba}-{gene|protein|card|vfdb}-detailed-summary.txt	Detailed information about each hit against a specific antimicrobial resistance or Ariba dataset
{amrfinder|ariba}-{gene|protein|card|vfdb}-summary.txt	A presence/absence matrix for hits against a specific antimicrobial resistance or Ariba dataset
lactobacillus-exclude.txt	A list of samples and the reason they failed quality cutoffs
lactobacillus-report.txt	A tab-delimited file containing sequence, assembly and annotation stats for all samples
lactobacillus-summary.txt	Brief breakdown of ranks and qc-failures

figures\files\tables Folders

└── figures
    ├── figure-1a-bactopia-overview.png
    ├── figure-1b-bactopia-workflow.pdf
    ├── figure-1b-bactopia-workflow.png
    ├── figure-1b-bactopia-workflow.svg
    ├── figure-2a-lactobacillus-16s.png
    ├── figure-2a-lactobacillus-16s.svg
    ├── figure-2b-lactobacillus-only-16s-annotated.png
    ├── figure-2b-lactobacillus-only-16s-annotated.svg
    ├── figure-2b-lactobacillus-only-16s.svg
    ├── figure-3-lcrispatus-core-genome-annotated.png
    ├── figure-3-lcrispatus-core-genome-annotated.svg
    ├── figure-3-lcrispatus-core-genome.svg
    ├── supplementary-figure-1-bactopia-workflow.pdf
    ├── supplementary-figure-1-bactopia-workflow.png
    ├── supplementary-figure-1-bactopia-workflow.svg
    ├── supplementary-figure-2-quality-by-year.pdf
    ├── supplementary-figure-2-quality-by-year.png
    ├── supplementary-figure-3-genome-size-assembly-vs-estimate.pdf
    ├── supplementary-figure-3-genome-size-assembly-vs-estimate.png
    ├── supplementary-figure-4-consistent-genome-size.pdf
    └── supplementary-figure-4-consistent-genome-size.png
└──  files
    ├── supplementary-data-1-lactobacillus-query-results.txt
    ├── supplementary-data-2-illumina-accessions.txt
    └── supplementary-data-3-nextflow-report.html
└── tables
    ├── supplementary-table-1-samples-excluded.txt
    ├── supplementary-table-2-non-lactobacillus-by-gtdb.txt
    ├── table-1-list-of-bioinformatic-tools.txt
    ├── table-2-comparison-of-workflows.txt
    ├── table-3-lactobacillus-sequence-summary.txt
    └── table-4-lactobacillus-crispatus-metadata.txt

Filename / Directory	Description
figures	Figures used in preprint
files	Supplementary data in the preprint
tables	Tab-delimited representations of tables in the preprint

scripts Folder

└── scripts
    ├── bactopia-analysis.Rmd
    ├── bactopia-workflow-key.R
    ├── bactopia-workflow.R
    └── lactobacillus-analysis.sh

This directory contains the scripts used in this analysis.

Filename	Description
bactopia-analysis.Rmd	This is the primary script for analysis results, used to create bactopia-analysis.html
bactopia-workflow-key.R	Used to create the key for the Bactopia Workflow diagram
bactopia-workflow.R	Used to create the Bactopia Workflow diagram
lactobacillus-analysis.sh	Commands used to run Bactopia