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Added support for Canu and other assembler gfas

Open amanzanom opened this issue 1 year ago • 1 comments

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

amanzanom avatar Jul 18 '24 08:07 amanzanom