midas_species

Tags: metagenomics abundance species midas marker-genes diversity sample-scope

Estimate bacterial species abundance from metagenomic reads.

Uses MIDAS (Metagenomic Intra-Species Diversity Analysis System) to estimate the abundance of bacterial species in metagenomic data. It maps reads to a database of universal single-copy marker genes (15 genes) to provide accurate coverage and relative abundance estimates.

Uses explicit positional record fields for reads:

• Input: record(meta, r1, r2, se) where each read slot is Path?

Database Required

Requires a compatible MIDAS database (containing marker gene sequences and taxonomy).

Inputs

record (
    meta: Record,
    r1: Path?,
    r2: Path?,
    se: Path?
)

Field	Type	Description
meta	Record	Groovy Record containing sample information
r1	Path?	Illumina R1 reads (paired-end)
r2	Path?	Illumina R2 reads (paired-end)
se	Path?	Single-end Illumina reads

db: Path

Name	Type	Description
db	Path	Directory containing the MIDAS database

Outputs

record (
    meta: Record,
    tsv: Path,
    abundances: Path,
    adjusted_abundances: Path,
    results: Set<Path>,
    logs: Set<Path?>,
    nf_logs: Set<Path>,
    versions: Set<Path>
)

Field	Type	Description
meta	Record	Sample information record
tsv	Path	A tab-delimited summary of species abundance and coverage
abundances	Path	Detailed species abundance profile (*.abundances.txt)
adjusted_abundances	Path	Relative abundance estimates adjusted for genome size (*.adjusted.abundances.txt)
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

MIDAS Species Parameters

Parameter	Type	Default	Description
--midas_word_size	integer	28	Word size for BLAST search
--midas_aln_cov	number	0.75	Discard reads with alignment coverage < ALN_COV
--midas_opts	string		Extra MIDAS options
--midas_debug	boolean	false	Keep all temporary files created by MIDAS

Used By

Subworkflows

• midas - Species-level profiling from metagenomic data.

Workflows

• midas - Estimate species abundances from metagenomic samples.

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)

• MIDAS
  Nayfach S, Rodriguez-Mueller B, Garud N, and Pollard KS An integrated metagenomics pipeline for strain profiling reveals novel patterns of bacterial transmission and biogeography. Genome Research, 26(11), 1612-1625. (2016)

Source

View source on GitHub

Version

MIDAS_SPECIES:
    - midas: 1.3.2