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Welcome to the GenGraph wiki!

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Newly updated to Python3 and NetworkX 2.3.

Requirements

NetworkX 2.3

If pip is installed, simply:

pip install networkx

A Whole genome alignment tool Mauve Specifically, progressiveMauve.

At least one of the following:

• MAFFT (Recommended)
• Clustal Omega
• Muscle

Setup

(This needs updating)

To install GenGraph

pip install GenGraph

To run gengraphTool.py

Download gengraphTool.py file either by cloning the repository or downloading the .zip file.

python3 gengraphTool.py <tool> <commands>

Basic usage

To create a genome graph:

1. Create the sequence input file. This is a tab delimited file with 4 columns:

seq_name        aln_name        seq_path        annotation_path
H37Rv           seq0        <path to fasta file>        <path to annotation gff/NA>
CDC1551         seq1        <path to fasta file>        <path to annotation gff/NA>
F11             seq2        <path to fasta file>        <path to annotation gff/NA>

• The column seq_name is any name used to identify an isolate.
• The column aln_name always contains seq(x) where x starts at 0 and increases.
• The column seq_path is the absolute path to the genome fasta file.
• The column annotation_path is EITHER the absolute path to the annotation file in gff format OR the string NA if no annotation file is available or needed.

2. Run gengraphTool.py

python ./gengraphTool.py make_genome_graph --seq_file <sequence_input_file.txt> --out_file_name <file name>

To import a genome graph in python:

graph_obj = import_gg_graph(<path_to_GG_xml_file>)

Under development

• Generating a consensus sequence from raw reads
• Read mapping to the genome graph