MeReco : Large-scale Metabolic Reconstruction from bacterial genomes

Workflow to reconstruct multiple metabolic graphs directly from sequence fasta.

Table of contents

• License
• Installation
  • Dependencies
  • Installation of Pathway Tools
  • Getting the MetaCyc PADMET file
  • pip
• Usage

License

This workflow is licensed under the GNU GPL-3.0-or-later, see the LICENSE file for details.

Installation

Dependencies

These tools are needed:

• Prokka
• EggNOG-mapper
• Bakta
• Pathway Tools (which needs Blast)

And some python packages:

• mpwt
• padmet
• pandas

Installation of Pathway Tools

To run annotation based reconstruction, you need to install Pathway Tools. This tool is available at the Pathway Tools website.

Getting the MetaCyc PADMET file

You also should install the MetaCyc_XX.X.padmet (the version number of MetaCyc is replaced with XX.X), and then you should update your config.txt files for each study. This is the way to get a MetaCyc_XX.padmet file: Firstly, download the flat files of MetaCyc in DAT format at the https://biocyc.org/download.shtml webpage. Secondly, put all the downloaded DAT files in a directory (it is named FLAT_DIR here). Thirdly run this command:

padmet pgdb_to_padmet --pgdb=FLAT_DIR --output=metacyc_XX.X.padmet --version=XX.X --db=Metacyc -v

pip

If you have installed all the dependencies, you can just install MeReco with:

pip install mereco

Usage

metabolic_reconstruction.py [-h] -i INPUT -o OUTPUT --tax TAXFILE --padmet_ref PATH_TO_PADMET_REF --ptsc PTSC --ptsi PTSI [--annot ANNOT] [--egg_path EGG_PATH] [--bak_path BAK_PATH]
                            [-c CPUS] [-k TO_KEEP] [-q]

-k flag can be used to save some intermediary files from Prokka and Bakta (listed blow). To keep some specific files, mention their extension separated by ",", following the structure below :

Prokka : .ecn,.err,.ffn,.fixed*,.fsa,.gff,.log,.sqn,.tbl,.val,.faa Bakta : .embl,.faa,.ffn,.fna,.gff3,.hypotheticals.faa,.hypotheticals.tsv,.json,.log,.png,.svg,.tsv