BASIC PROTOCOL 2: Download MIDAS Reference Database

Abstract

This protocol describes how to download all or part of a MIDASDB, a set of custom files constructed from microbial genome sequences and containing all the information needed to metagenotype the species detected in a set of shotgun-metagenomic samples. MIDAS2 provides two prebuilt MIDASDBs sourced from large, public microbial genome collections: MIDASDB-UHGG (4,644 species / 286,997 genomes) based on the Unified Human Gastrointestinal Genome catalog (v1) [9] and MIDASDB-GTDB (47,893 species / 258,405 genomes) based on the Genome Taxonomy Database (v202) [10]. Support Protocol 2 describes how to build a new MIDASDB locally from a custom genome collection. A MIDASDB should be downloaded or built before any other MIDAS2 protocols can be run.

There are three components in a MIDASDB: single-copy marker genes (SCGs), representative genomes (rep-genome), and pangenomes (pan-genome). Each species contributes sequences to all three components. By preloading the MIDASDB, individual calls to MIDAS2 commands do not need to automatically download the necessary files. As a result, with a preloaded MIDASDB, per-sample analyses can be run in parallel without a risk of processes interfering with one another.

Steps

Initialize a local copy of MIDASDB-UHGG

midas2 database --init --midasdb_name uhgg --midasdb_dir midasdb_uhgg

Note

This command creates the local directory midasdb_uhgg/ if it doesn’t exist, and downloads the following files/directories:genomes.tsv: the table-of-contents file assigning genomes to species and denoting the representative genome for each species.metadata.tsv: tab-deliminated table specifying the six-digit numeric species identifiers (species_id) with taxonomic assignments.md5sum.json: md5sum cache for database files; used internally by MIDAS2 during downloading.markers/: SCG data needed for species prescreening.markers_models/: SCG profile hidden Markov model.chunks/: design cache for parallelizing the SNV module over partitions of the representative genome (“chunks”).

Customize the MIDASDB download. In Basic Protocol 1, 22 species were present in at least one sample list_of_species.tsv). Now those will be downloaded in the database components (both rep-genome and pan-genome) only for these 22 species.

midas2 database --download --midasdb_name uhgg --midasdb_dir midasdb_uhgg --species_list list_of_species.tsv

The download has completed successfully when the command midas2 database --download finishes and no error is reported.

Abstract

Steps

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