gapseq

name	gapseq
description	Predict bacterial metabolic pathways and reconstruct genome-scale metabolic models. Use this skill when working with gapseq: installing, choosing parameters, running commands, interpreting outputs, or troubleshooting. Upstream: https://github.com/jotech/gapseq. For routing across mining tasks use microbial-mining. For stage order use metagenomics-workflow.
license	MIT
category	analysis-tools
tags	["metabolism","GEMs","genome-mining"]
upstream	https://github.com/jotech/gapseq
stage	mining

gapseq

Upstream: gapseq

Citation

Zimmermann, J., Kaleta, C. & Waschina, S. gapseq: informed prediction of bacterial metabolic pathways and reconstruction of accurate metabolic models. Genome Biol. 22, 81 (2021). https://doi.org/10.1186/s13059-021-02295-1

See also docs/references.md.

Analytical thinking

Downstream of genome annotation for pathway/model mining. Needs reasonably complete MAGs; low-completeness bins produce hollow models. Interpret human/gut context with vmh when relevant.

How to run

conda install -c bioconda gapseq  # if packaged; else follow upstream docs

gapseq find -p all genome.fa
gapseq draft -r genome -c genome-draft.RDS -p genome-all-Reactions.tbl -b 136
gapseq fill -m genome-draft.RDS -n genome-Medium.csv -c genome-rxnWeights.RDS -n genome-rxnXgenes.RDS

Key parameters

| completeness | prefer high-quality MAGs | | | pathways | -p all costly | |

Decision notes

• Run mining on QC-filtered genomes/MAGs (or contigs for MGE/virus screens)
• Computational hits are hypotheses — state validation limits in Methods
• Pin software + database releases

Related skills

dram · bakta · checkm2 · eggnog-mapper · microbial-mining · tool-selection · metagenomics-workflow vmh