gapseq reconstructions for 5414 genomes from the HRGM collection

The data set contains genome-scale metabolic network reconstructions for 5414 microbial genomes from the Human Reference Gut Microbiome (HRGM) collection (doi: 10.1186/s13073-021-00950-7). Reconstructions were made using gapseq (development version 1.1, commit: 564668f).

When using the models, please cite:

1. Kim, C.Y., Lee, M., Yang, S. et al. Human reference gut microbiome catalog including newly assembled genomes from under-represented Asian metagenomes. Genome Med 13, 134 (2021). DOI: 10.1186/s13073-021-00950-7
2. Zimmermann, J., Kaleta, C. & Waschina, S. gapseq: informed prediction of bacterial metabolic pathways and reconstruction of accurate metabolic models. Genome Biol 22, 81 (2021). DOI: 10.1186/s13059-021-02295-1

The models were reconstructed using the following workflow.

# Reaction & Pathway prediction
./gapseq find -b 200 -v 1 -p all -k -t <Bacteria|Archaea> <genomeID>.fna.gz

# Transporter prediction
./gapseq find-transport -b 200 -k <genomeID>.fna.gz

# Draft network reconstruction
./gapseq draft -r <genomeID>-all-Reactions.tbl -t <genomeID>-Transporter.tbl -b <Bacteria|Archaea> -c <genomeID>.fna.gz -p <genomeID>-all-Pathways.tbl -u 200 -l 100

# gapfill/growth medium prediction
./gapseq medium -m <genomeID>-draft.RDS -p <genomeID>-all-Pathways.tbl -c "cpd00007:0"

# Gap-filling
# (If H2 is part of the medium)
./gapseq fill -m <genomeID>-draft.RDS -n <genomeID>-medium.csv -c <genomeID>-rxnWeights.RDS -g <genomeID>-rxnXgenes.RDS -b 100 -e highH2
# (If H2 is not part of the medium)
./gapseq fill -m <genomeID>-draft.RDS -n <genomeID>-medium.csv -c <genomeID>-rxnWeights.RDS -g <genomeID>-rxnXgenes.RDS -b 100