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: 1.2, commit 13d88a68; Sequence DB md5sum: bf8ba98 (2021-06-02, Bacteria).

When using the models, please cite:

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

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 .fna.gz

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

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

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

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

Please note that the model collection contains 2 additional genome-scale metabolic for genomes, that are not part of the HRGM collection:

NISW_Genome_0001 (Assembly: GCF_007164725.1, Species: Dialister hominis)

NISW_Genome_0002 (Assembly: GCF_000296465.1, Species: Barnesiella intestinihominis)