Can we use megahit to assemble rna-seq data?

voutcn / megahit

Ultra-fast and memory-efficient (meta-)genome assembler

http://www.ncbi.nlm.nih.gov/pubmed/25609793

GNU General Public License v3.0

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Can we use megahit to assemble rna-seq data? #332

Open xiekunwhy opened 2 years ago

xiekunwhy commented 2 years ago

Hi,

Can we use megahit as a denovo assembler to assemble rna-seq data?

Best, Kun

WJT0925 commented 2 years ago

I have the same question， and I test trinity and megahit using the same metatranscriptomes pair-data about 50G, and the result shows a longer N50 assembly by megahit, also use more data than trinity, and both two result mapping rate similar, BUSCO of megahit was 96.5%, for trinity was 98%, so I think it maybe ok for metatranscriptoms.

aquaskyline commented 2 years ago

Yes, megahit works with RNA-seq data, or any other ununified depth data.