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NVlabs / nvbio

NVBIO is a library of reusable components designed to accelerate bioinformatics applications using CUDA.
BSD 3-Clause "New" or "Revised" License
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nvBWT (and nvSetBWT) do not deal with multifasta (treats only first ref into) #44

Open FTouzain opened 3 years ago

FTouzain commented 3 years ago

Hello,

When indexing a multifasta file, both nvBWT and nvSetBWT work, but they treat only the first sequence in my multifasta file. (nvBowtie works also, treating this only first reference sequence).

How to deal with multifasta (therefore several fasta sequences in a same file), please? Thank you in advance.

dnbuckley commented 2 years ago

I also have this issue.

andreirajkovic commented 2 years ago

Any updates on this?

andrewmoeller commented 2 years ago

I agree that it would be great if these tools were applicable to multifasta files, particularly because it would allow the tools to be used in metagenomics studies. One area where it could be particularly helpful is assembling genomes from metagenomes. The current approaches can incorporate information about the relative abundances of contigs across samples into the binning process, but typically this is only done for a small number of samples due to reliance on cpu-based mapping software. Extending the nv tools to work with multifastas could be a huge advance!