midas

Tags: metagenomics species-abundance profiling midas bactopia-tool

Estimate species abundances from metagenomic samples.

This Bactopia Tool uses MIDAS to estimate bacterial species abundances in metagenomic samples. MIDAS uses a database with more than 30,000 reference genomes for accurate species profiling.

Usage

Bactopia CLI:

bactopia --wf midas \
  --bactopia /path/to/your/bactopia/results

Nextflow:

nextflow run bactopia/bactopia/workflows/bactopia-tools/midas/main.nf \
  --bactopia /path/to/your/bactopia/results

Outputs

Expected Output Files

<BACTOPIA_DIR>
├── <SAMPLE_NAME>
│   └── tools
│       └── midas-<TIMESTAMP>
│           ├── <SAMPLE_NAME>.midas.abundances.txt
│           ├── <SAMPLE_NAME>.midas.adjusted.abundances.txt
│           ├── <SAMPLE_NAME>.midas.tsv
│           └── logs
│               ├── nf.command.{begin,err,log,out,run,sh,trace}
│               └── versions.yml
└── bactopia-runs
    └── midas-<TIMESTAMP>
        ├── merged-results
        │   ├── logs
        │   │   └── midas-concat
        │   │       ├── nf.command.{begin,err,log,out,run,sh,trace}
        │   │       └── versions.yml
        │   └── midas.tsv
        └── nf-reports
            ├── midas-dag.dot
            ├── midas-report.html
            └── midas-timeline.html

Species Abundance

File	Description
*.tsv	Species abundance profiles
*-species.tsv	Species-level abundance
*-genes.tsv	Gene-level abundance

Merged Results

File	Description
midas.tsv	Merged TSV file containing MIDAS results from all samples

Audit Trail

Below are files that can assist you in understanding which parameters and program versions were used.

Logs

Each process that is executed will have a folder named logs. In this folder are helpful files for you to review if the need ever arises.

Extension	Description
.begin	An empty file used to designate the process started
.err	Contains STDERR outputs from the process
.log	Contains both STDERR and STDOUT outputs from the process
.out	Contains STDOUT outputs from the process
.run	The script Nextflow uses to stage/unstage files and queue processes based on given profile
.sh	The script executed by bash for the process
.trace	The Nextflow trace report for the process
versions.yml	A YAML formatted file with program versions

Nextflow Reports

These Nextflow reports provide great a great summary of your run. These can be used to optimize resource usage and estimate expected costs if using cloud platforms.

Filename	Description
midas-dag.dot	The Nextflow DAG visualization
midas-report.html	The Nextflow Execution Report
midas-timeline.html	The Nextflow Timeline Report
midas-trace.txt	The Nextflow Trace report

Parameters

Required Parameters

Define where the pipeline should find input data and save output data.

Parameter	Type	Default	Description
--bactopia	string		The path to bactopia results to use as inputs

MIDAS Database Download Parameters

Parameter	Type	Default	Description
--midas_db	string		A single tarball or path to a MIDAS formatted database
--midas_save_as_tarball	boolean	false	Save the MIDAS database as a tarball
--download_midas	boolean	false	Download the MIDAS database to the path given by --midas_db

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

Filtering Parameters

Use these parameters to specify which samples to include or exclude.

Parameter	Type	Default	Description
--include	string		A text file containing sample names (one per line) to include from the analysis
--exclude	string		A text file containing sample names (one per line) to exclude from the analysis

Optional Parameters

These optional parameters can be useful in certain settings.

Parameter	Type	Default	Description
--outdir	string	bactopia	Base directory to write results to

Nextflow Profile Parameters

Parameters to fine-tune your Nextflow setup.

Parameter	Type	Default	Description
--datasets_cache	string	<HOME>/.bactopia/datasets	Directory where downloaded datasets should be stored.

Helpful Parameters

Uncommonly used parameters that might be useful.

Parameter	Type	Default	Description
--wf	string	bactopia	Specify which workflow or Bactopia Tool to execute
--list_wfs	boolean		List the available workflows and Bactopia Tools to use with '--wf'
--help_all	boolean		An alias for --help --show_hidden_params
--version	boolean		Display version text.

Composition

This workflow uses the following subworkflows:

• midas - Species-level profiling from metagenomic data.

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