README.md

GMGC data downloaded from https://gmgc.embl.de

This repository collects Global Microbial Gene Catalog (GMGC) sequence data, which store separately according to sequence length.

Data statistics

The number of sequences is shown below:

Length $L$	Built environment	Cat gut	Dog gut	Freshwater	Human gut	Human nose	Human oral	Human skin	Human vagina	Marine	Mouse gut	Pig gut	Soil	Wastewater	After deduplication
$5000 \leq L \leq 10000$	10423	11694	9221	1853	82549	10786	33935	33167	5261	28914	5222	32600	10568	12775	153270
$10000 \leq L \leq 20000$	2263	922	859	488	8587	886	2908	3987	330	3338	512	3512	1306	1627	16557
$20000 \leq L \leq 30000$	1347	875	190	57	2128	996	1000	1463	28	396	80	600	185	392	2891
$30000 \leq L \leq 40000$	2149	1913	1	1	2338	2187	1921	2163	0	38	7	63	229	3	2459
$L \geq 40000$	11	1	0	0	122	68	0	51	0	6	11	2	9	2	179

How to use data

All data in this repository has zipped by xz except dedup/5000.zip. Use xz in unix system to decompress files.

For file dedup/5000.zip, use the following command:

cat dedup/5000.z* > dedup/5000_final.zip
unzip dedup/5000_final.zip

The folder of datasets is shown below:

Dataset name	Folder name
Built environment	built-env
Cat gut	cat-gut
Dog gut	dog-gut
Freshwater	freshwater
Human gut	human-gut
Human nose	human-nose
Human oral	human-oral
Human skin	human-skin
Human vagina	human-vagina
Marine	marine
Mouse gut	mouse-gut
Pig gut	pig-gut
Soil	soil
Wastewater	wastewater
After deduplication	dedup

Ciation

Coelho, L.P., et al. Towards the biogeography of prokaryotic genes. Nature 601, 252–256 (2022).