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COMBINE-lab / cuttlefish

Building the compacted de Bruijn graph efficiently from references or reads.
BSD 3-Clause "New" or "Revised" License
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Reduced GFA output --> GFA1/GFA2 Output #37

Open aryakaul opened 10 months ago

aryakaul commented 10 months ago

Hello!

Thanks for Cuttlefish, it's been working nicely for me so far. I've been using the reduced GFA format for my own analysis, but have occasionally come across tools that demand the more accepted GFA1/GFA2 file specifications. I was wondering if y'all had a script or manner to transform the reduced GFA output format into the other formats? No worries if not, but would rather not write one if it's already coded somewhere.

Best, Arya

jamshed commented 10 months ago

Hi @aryakaul: good to know you're finding Cuttlefish useful!

You're right—the GFA 1/2 formats are standardized graph representation formats and used in many tools. And actually the reduced GFA format is a Cuttlefish-specific format, devised for efficiency concerns, as discussed here.

Unfortunately we do not yet have a script to convert to-and-from the reduced GFA format. If you happen to write one, please make a PR here if possible!

Best regards.