GenGraph

A repository for the GenGraph toolkit for the creation and manipulation of graph genomes

This project aims to make genome graphs simple to create, and provide tools for their manipulation and intergration into common workflows.

Please refer to the wiki for installation and usage instructions.

Quickstart

python3 ./gengraphTool.py make_genome_graph --seq_file <sequence_file.txt> --out_file_name <filename> --recreate_check

A Docker file is also available that will contain everything you need for your first run.

Sequence file

The sequence file is a tab delimited file with 4 columns:

seq_name	aln_name	seq_path	annotation_path
H37Rv	seq0	/Users/panix/Desktop/genomes/H37Rv/sequence.fasta	NA
Beijing	seq1	/Users/panix/Desktop/genomes/Beijing-NITR203/sequence.fasta	NA
H37Ra	seq2	/Users/panix/Desktop/genomes/H37Ra/sequence.fasta	NA

The seq_name column is used as the node and edge 'ids' attribute value. It needs to be unique.