midas
Tags: metagenomics species profiling abundance strain sample-scope
Species-level profiling from metagenomic data.
This subworkflow estimates strain-level genomic variation from metagenomic data using MIDAS. The pipeline identifies bacterial species abundances and provides strain-level profiling including SNP analysis. It uses a comprehensive reference database for accurate species identification and quantification in complex microbial communities.
Uses explicit positional record fields for reads:
- Input: record(meta, r1, r2, se, lr) where each read slot is Path?
Take
reads: Channel<Record>
| Field | Description |
|---|---|
meta | Groovy Record containing sample information |
r1 | Illumina R1 reads (paired-end) |
r2 | Illumina R2 reads (paired-end) |
se | Single-end Illumina reads |
lr | Long reads (not supported by MIDAS) |
database: Path?
download_midas: Boolean
save_as_tarball: Boolean
| Name | Type | Description |
|---|---|---|
database | Path? | MIDAS reference database for species identification and quantification |
download_midas | Boolean | Boolean flag to automatically download the MIDAS database if not available |
save_as_tarball | Boolean | Boolean flag to save downloaded database as tarball |
Emit
Published
The sample_outputs and run_outputs emissions are aggregates of output files that will be published in the entry workflow.
sample_outputs
| Output | Description |
|---|---|
tsv | A tab-delimited summary of species abundance and coverage |
abundances | Detailed species abundance profile |
run_outputs
| Output | Description |
|---|---|
csv | Merged species abundance results from all samples |
Module Composition
This subworkflow calls the following modules:
- csvtk_concat - Concatenate multiple CSV or TSV files into a single table.
- midas_species - Estimate bacterial species abundance from metagenomic reads.
- midas_download - Download the MIDAS reference database.
Used By
This subworkflow is used by the following 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)