bactopia_teton

Tags: taxonomy genome-size routing filtering bacteria sizemeup bracken sample-scope

Predict genome size and route samples based on taxonomic classification.

Uses SizeMeUp to parse Bracken abundance reports, estimate the genome size for the identified species, and split samples into "Bacteria" (for downstream analysis with Bactopia) and "Non-Bacteria" lists.

Inputs

record (
    meta: Record,
    classification: Path
)

Field	Type	Description
meta	Record	Groovy Record containing sample information
classification	Path	Bracken species abundance report

Outputs

record (
    meta: Record,
    bacteria_tsv: Path,
    nonbacteria_tsv: Path,
    sizemeup: Path,
    results: Set<Path>,
    logs: Set<Path?>,
    nf_logs: Set<Path>,
    versions: Set<Path>
)

Field	Type	Description
meta	Record	Sample information record
bacteria_tsv	Path	A tab-delimited samplesheet compatible with Bactopia (--samples) for samples identified as Bacteria
nonbacteria_tsv	Path	A tab-delimited samplesheet for samples NOT identified as Bacteria
sizemeup	Path	A text file containing the predicted species and genome size
results	Set<Path>	All output files to be published
logs	Set<Path?>	Optional program specific log files
nf_logs	Set<Path>	Nextflow-specific log files (e.g. .command.{begin
versions	Set<Path>	A YAML formatted file with program versions

Parameters

Used By

Subworkflows

• teton - Perform taxonomic classification and estimate bacterial genome sizes.

Workflows

• teton - Taxonomic classification and abundance profiling of metagenomic reads.

Citations

If you use this in your analysis, please cite the following.

• Bactopia
  Petit III RA, Read TD Bactopia - a flexible pipeline for complete analysis of bacterial genomes. mSystems 5 (2020)

• Bracken
  Lu J, Breitwieser FP, Thielen P, and Salzberg SL Bracken: estimating species abundance in metagenomics data. PeerJ Computer Science, 3, e104. (2017)

• sizemeup
  Petit III RA sizemeup: A simple tool to retrieve the genome size for a given species name or tax ID (GitHub)

Source

View source on GitHub

Version

BACTOPIA_TETON:
    - bactopia-teton: 1.1.3