Hologenomes

Use ehitk hologenomes to find shotgun metagenomic sequencing datasets and download paired-end reads.

Query hologenomes

ehitk hologenomes query --hologenome-id EHI00001
ehitk hologenomes query --host-species "Podarcis muralis"
ehitk hologenomes query --host-taxid 8509
ehitk hologenomes query --host-lineage Reptilia
ehitk hologenomes query --sample-type Faecal --biome-name "Temperate woodland"
ehitk hologenomes query --biome ENVO:01000175
ehitk hologenomes query --data-min 5 --data-max 25
ehitk hologenomes query --country Italy --latitude-min 42.7 --latitude-max 42.8
ehitk hologenomes query --hologenome-id EHI00001,EHI00002

Filters

--hologenome-id: Exact hologenome ID. Comma-separated values are accepted.
--host-taxid, --host-species, --host-lineage: Host taxonomy filters. --host-taxid accepts NCBI taxon identifiers and includes catalog descendants, so 8509 matches Squamata host species. --host-lineage matches species, genus, family, order, or class.
--sample-type: Exact sample metadata label.
--biome-envo-id/--biome and --biome-name: Biome filters. ENVO identifier filters include catalog descendants, so ENVO:01000175 matches woodland biome subclasses such as ENVO:01000221. --biome-name matches the human-readable biome name exactly.
--country: Exact country label.
--release: Exact EHI release ID.
--data-min and --data-max: Minimum and maximum available data volume in gigabases.
--latitude-min, --latitude-max, --longitude-min, --longitude-max: Coordinate range filters.
--weight-min, --weight-max, --length-min, --length-max: Linked specimen measurement filters.

Summarize hologenomes

ehitk hologenomes stats --host-species "Podarcis muralis"
ehitk hologenomes fields
ehitk hologenomes values --field host_species
ehitk hologenomes values --field biome_name
ehitk hologenomes values --field country --limit 20
ehitk hologenomes values --field data_gb --limit 10

Download hologenomes

ehitk hologenomes fetch downloads paired-end reads from url1 and url2. Records with missing read URLs are skipped.

ehitk hologenomes fetch --host-species "Podarcis muralis" --limit 1
ehitk hologenomes fetch --release EHR01 --limit 1 --batch hologenomes.sh

Available query columns

hologenome_id, 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.