This is a simple tool for converting IDBA assemblies into GFA graphs. This allows the graphs to be loaded into Bandage or anything else which accepts GFA files.

It was made my myself and Matt Olm.

It's just a single Python 3 script, so no installation is required. It uses the print_graph tool (which is built along with IDBA), so that must be installed on the same computer.

usage: idba_to_gfa.py [-h] [--print_graph PRINT_GRAPH] idba_assembly kmer

IDBA to GFA: a tool for converting IDBA assemblies to GFA graphs

positional arguments:
  idba_assembly         Assembly from IDBA, e.g. scaffold.fa
  kmer                  assembly k-mer size (e.g. 100)

optional arguments:
  -h, --help            show this help message and exit
  --print_graph PRINT_GRAPH
                        Location of IDBA's print_graph tool (required if
                        print_graph is not in PATH)

output: GFA to stdout

Build a 100-mer graph from IDBA scaffolds:
idba_to_gfa.py scaffold.fa 100 > scaffold_100.gfa

Build an 80-mer graph from IDBA contigs:
idba_to_gfa.py contig.fa 80 > contig_80.gfa

Give the location of print_graph (necessary if it's not in PATH):
idba_to_gfa.py --print_graph /path/to/idba-1.1.3/bin/print_graph scaffold.fa 100 > scaffold_100.gfa

GNU General Public License, version 3