midas_download

Tags: midas download database metagenomics species run-scope

Download the MIDAS reference database.

Fetches the pre-compiled database required by MIDAS for metagenomic species profiling. The database contains reference genomes from the UHGG collection used for species identification and abundance estimation.

Internet & Storage Required

This process requires an active internet connection and significant disk space to store the database files (~3.3GB compressed, ~7GB uncompressed).

Outputs

record (
    db: Path?,
    db_tarball: Path?,
    logs: Set<Path?>
)

Field	Type	Description
db	Path?	The MIDAS database directory containing reference genome data
db_tarball	Path?	A compressed tarball of the database (if requested via parameters)
logs	Set<Path?>	Optional program specific log files

Parameters

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

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_DOWNLOAD:
    - gnu-wget: 1.18