Published October 26, 2022 | Version v1
Dataset Open

Pre-computed MGCs from human microbiome reference genomes

Creators

  • 1. Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
  • 2. Bioinformatics Group, Wageningen University, Wageningen, The Netherlands; University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, Netherlands
  • 3. University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, Netherlands; University of Groningen, University Medical Center Groningen, Department of Pediatrics, Groningen, Netherlands
  • 4. University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, Netherlands
  • 5. Department of Bioengineering, Stanford University, Stanford, USA; Department of Microbiology & Immunology, Stanford University, Stanford, USA; Chan Zuckerberg Biohub, San Francisco, CA USA
  • 6. Department of Microbiology & Immunology, Stanford University, Stanford, USA; Department of Pathology, Stanford University, Stanford, USA

Description

This dataset contains non-redundant metabolic gene clusters (MGCs) collected by running gutSMASH and BiG-MAP on a collection of unique high-quality reference genomes. This collection consist of MGCs predicted by gutSMASH using 1,520 genomes from the Culturable Genome Reference (CGR), 2,308 genomes from the Human Microbiome Project (HMP) and 414 Clostridia genomes as input and then filtered for redundancy using the family module of BiG-MAP. For more information: https://doi.org/10.1101/2021.02.25.432841

BiG-MAP_mg.pickle -> suitable for metagenome analyses

BiG-MAP_mt.pickle -> suitable for metatranscriptome analyses

The files can be used as direct input in the third module of BiG-MAP (BiG-MAP.map.py: https://github.com/medema-group/BiG-MAP).

Files

Files (376.5 MB)

Name Size Download all
md5:c2de83e0ff53dad6f36f064c9070765b
177.6 MB Download
md5:63366ab081469c773128c2599c79606f
198.9 MB Download

Additional details

Related works

Is derived from
Preprint: 10.1101/2021.02.25.432841 (DOI)
Is required by
Journal article: 10.1128/mSystems.00937-21 (DOI)