Dataset Open Access

Artifacts for q2-micom

Diener, Christian

This repository hosts artifacts for use with q2-micom and MICOM. In particular it provides summarized metabolic model databases and growth media.

 

Model databases

Model databases are provided for family, genus and species ranks. AGORA is a manually curated database of 818 high quality metabolic reconstructions. Raw data was obtained from https://www.vmh.life/.

CarveME is an automatically reconstructed database but offers much more organisms (>5K strains). Raw data was obtained from https://github.com/cdanielmachado/embl_gems.

 

Diets

We currently only provide an average western diet which is only compatible with AGORA.

 

 

Files (1.1 GB)
Name Size
agora103_family.qza
md5:20ce58f32bed50181004f0a4a2a97934
10.1 MB Download
agora103_genus.qza
md5:bb08b2ca4761f2f64c82ba926bf9c39f
21.1 MB Download
agora103_species.qza
md5:ddec06f45acb24774ba68dda97ff2804
50.0 MB Download
carveme_refseq84_family.qza
md5:b4d104c8ef1ce12a737ff84c5cb43c8b
68.6 MB Download
carveme_refseq84_genus.qza
md5:41386026ec4232feb472502ad92f8753
264.3 MB Download
carveme_refseq84_species.qza
md5:59f08a29ae4075570c1c300552982770
693.1 MB Download
western_diet_gut.qza
md5:ab1602ec728a95105b420354b5b30a93
7.2 kB Download
  • Diener et. al. Additional data related to https://doi.org/10.1101/361907.

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