Metagenomic database utilities

This repository contains scripts used to create metagenomic databases for metaproteomic analysis as part of the analysis for the ConDiGA repository.

File organisation

metagenomic-database-utilities
│   environment.yml   
│   LICENSE
│   README.md 
│
└───scripts
│   │   assemble.sh
│   │   coverm.sh
│   │   kraken2.sh
│   │   metagenemark.sh
│   
└───notebooks
    │   MD1_UniProt12.ipynb
    │   MD2_UniProt12.ipynb
    │   MD3_UniProt12.ipynb

The scripts use to run other software for assembly, taxonomic classification, gene prediction and coverage calculation are found in the scripts folder.

The steps and code used to create MD1, MD2 and MD3 databases can be found in the respective notebooks in the notebooks folder.

Contacts

Please report any problems in the issue tracker. Also, you can send feedback to liang_qiao@fudan.edu.cn or yu.lin@anu.edu.au.