Description

Complete gapseq workflow from genome to gap-filled model

Input

Name
Description
Pattern

0 ()

1 ()

2 ()

db (directory)

Optional gapseq reference sequence database directory (from GAPSEQ_REQUESTDB). Passed to gapseq via -D. If not provided, gapseq downloads the database itself.

gapseq_db

Output

Name
Description
Pattern

0 ()

0 ()

0 ()

0 ()

0 ()

0 ()

Tools

gapseq Documentation

gapseq is designed to combine metabolic pathway analysis with metabolic network reconstruction and curation. The doall command runs the complete workflow: pathway prediction, transporter inference, model construction, and gap filling.

https://github.com/jotech/gapseqdoi: 10.1186/s13059-021-02295-1License: AGPL-3.0-only
Authors