Output the contig overlap graph in GFA format

bioinfologics / w2rap-contigger

An Illumina PE genome contig assembler, can handle large (17Gbp) complex (hexaploid) genomes.

http://bioinfologics.github.io/the-w2rap-contigger/

MIT License

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Output the contig overlap graph in GFA format #8

Closed sjackman closed 5 years ago

sjackman commented 8 years ago

Graphical Fragment Assembly (GFA) format describes the contig overlap graph of a genome sequence assembly. Bandage can be used to visualize this graph. The format specification was originally drafted by Heng Li and is now community-maintained and nearing completeness. The format allows optional fields similarly to the SAM spec.

bjclavijo commented 8 years ago

Hi Shaun, I am working on this, it is actually quite helpful to use GFA as an exchange format. Next updated version (quite soon, I hope) will have some GFA support, even if not perfect.

bjclavijo commented 8 years ago

Leaving this open till the support is on the main branch and tested...

sjackman commented 8 years ago

That's great! Thanks, Bernardo. I'm excited to see more interoperability between assembler pipelines.

bjclavijo commented 5 years ago

This functionality is provided by hbv2gfa in older branches and will be provided directly in the next release.