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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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Any plans to implement scaffolding/gap filling? #260

Open edgardomortiz opened 4 years ago

edgardomortiz commented 4 years ago

I understand the main goal of MEGAHIT is metagenome assembly but I found it very useful for regular assemblies as well. I tried SOAPdenovo-fusion with results that look promising, but unfortunately the process is not very straightforward (e.g. can only be compiled in LINUX and even there has compilation problems), it hasn't been maintained in a while and is slow compared to the assembly speed of MEGAHIT.

If scaffolding will never be a feature of MEGAHIT, is there any other alternative to SOAPdenovo-fusion that can be recommended?

Anyway, thanks for the amazing software!

Edgardo

voutcn commented 4 years ago

I don't have any plans to implement a scaffolding software package. But not sure whether my co-authors have such a plan. @aquaskyline could you answer the question?