search

metagentools / GraphBin2

☯️🧬 Refined and Overlapped Binning of Metagenomic Contigs Using Assembly Graphs
https://graphbin2.readthedocs.io/en/latest/
BSD 3-Clause "New" or "Revised" License
33 stars 3 forks source link

Added support for Canu and other assembler gfas #21

Open amanzanom opened 2 months ago

amanzanom commented 2 months ago

I have already requested this for GraphBin, but would be great to get it in GraphBin2 and also in metaCoAG (great tools). Whenever trying to run GraphBin with an assembly graph coming from Canu, I keep getting the error when reading the reads " ERROR - Unexpected 'tig00XXXXX-XX-XXXXX' ". [....] Please make sure you have provided the correct assembler type and the correct path [....]. I imagine same issue will happen when trying to run GraphBin2 and metaCoAG.

I imagine there is no inherent problem in reading graphs from other assemblers, especially if coverage information is calculated separately. So, could you implement something in this line to be able to read other assembly graphs? I can provide you with an assembly graph I am using as an example.

I believe this can help widen the compatible assembly pipelines to use this software (which i think works really nicely). It would great to ahve this improvement soon ( =) ), as I am currently working on a large dataset like this in which I want to use GraphBin/metaCOAG.... otherwise, I'll need ot figure out other tools...

Cheers

Vini2 commented 2 months ago

Hello @amanzanom,

Thanks for your interest in GraphBin. I'm currently working on implementing support for other assemblers. Will update you soon regarding the new release.

Thanks, Vijini