MAGs

Use ehitk mags to find metagenome-assembled genomes. MAG records are linked to parent hologenomes, so MAG queries can also use host taxonomy, geography, and specimen measurement filters.

Query MAGs

ehitk mags query --quality high
ehitk mags query --quality high,medium
ehitk mags query --mag-id EHM00001
ehitk mags query --genus Escherichia
ehitk mags query --species "Escherichia coli"
ehitk mags query --host-species "Sciurus carolinensis"
ehitk mags query --host-taxid 40674
ehitk mags query --biome ENVO:01000175
ehitk mags query --hologenome-id EHI00392
ehitk mags query --country Italy --weight-min 630 --weight-max 690

Filters

--mag-id

Exact MAG ID. Comma-separated values are accepted.

--quality

Derived MAG quality class. Accepted values are high, medium, and low. Comma-separated values are accepted.

--genus and --species

Exact MAG taxonomy. EHItk normalizes GTDB-style g__ and s__ prefixes, so --genus Escherichia also matches g__Escherichia.

--host-taxid, --host-species, --host-lineage

Linked host taxonomy filters. --host-taxid is an NCBI host taxon identifier filter and includes catalog descendants. MAG taxonomy itself is still filtered with --genus and --species.

Taxonomy output

The default MAG query output includes the host NCBI host_taxid together with host species, genus, and family names, plus MAG family, genus, and species labels. MAG taxonomic labels come from GTDB-style MAG assignments; NCBI taxon identifiers are therefore reported for hosts, but not inferred for MAG taxa.

--biome-envo-id/--biome and --biome-name

Linked parent-hologenome biome filters. ENVO identifier filters include catalog descendants; biome name filters are exact.

Geography filters

Linked sampling geography filters.

Options: --country, --latitude-min, --latitude-max, --longitude-min, and --longitude-max.

--release

Exact MAG release ID.

--hologenome-id

Exact parent hologenome ID.

--weight-min, --weight-max, --length-min, --length-max

Linked specimen measurement filters.

MAG quality classes

high

completeness >= 90 and contamination <= 5.

medium

completeness >= 50 and contamination <= 10.

low

Records that do not meet the medium threshold.

Summarize MAGs

ehitk mags stats --quality high --species "Escherichia coli"
ehitk mags stats --host-species "Sciurus carolinensis"
ehitk mags fields
ehitk mags values --field genus
ehitk mags values --field species
ehitk mags values --field quality

Download MAGs

ehitk mags fetch downloads the MAG FASTA from url.

ehitk mags fetch --host-lineage Mammalia --quality high --limit 3
ehitk mags fetch --quality high --limit 10 --batch mags-downloads.sh

Available query columns

mag_id, release, quality, completeness, contamination, size, gc, n50, contigs, mag_domain, mag_phylum, mag_class, mag_order, mag_family, mag_genus, url, mag_species, hologenome_id, hologenome_release, sample_type, latitude, longitude, country, date, url1, url2, biome_envo_id, biome_name, data_gb, specimen_id, host_taxid, host_species, host_genus, host_family, host_order, host_class, weight, length, and sex.