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loneknightpy / idba

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IDBA-UD for low coverage eukaryote genome #31

Open dcopetti opened 7 years ago

dcopetti commented 7 years ago

Hello, I found that this software was used to assemble a polyploid plant and I am wondering if it could work as well in my case. I have 4 plant genomes (sequenced at about 20x, PE libraries up to 450 bp, 2x100 or 2x150 bp) that are from 1 to 1.4 Gb in size and are heterozygous. I assembled them with Meraculous (with some scaffolding and gap closing) and I can assemble 50-80% of the size, while the scaffold N50 is between 5 and 12 kb. Do you think this tool will work well? Will I need to run some error correction? I am a bit reluctant since the coverage is quite low. Shall I still try scaffolding and closing gaps after a IDBA-UD run? Thanks, Dario

lpryszcz commented 7 years ago

I've never tried IDBA with that low coverage, but I guess you could try. Also, you can try post-assembly improvement with https://github.com/lpryszcz/redundans