Question

recommendations for DeNovo assembly of short reads

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6.3 years ago

Phismil ▴ 20

Dear Colleagues , I have been away from the field for a while. I am wondering if you have any recommendations regarding a package to assemble de novo Illumina 2X250 reads in to contigues/scaffolds ? In my time Velvet was very popular. There are probably new tools around that I am unaware of them. Many thanks in advance

Denovo assembly software shortreads • 2.2k views

ADD COMMENT • link updated 6.2 years ago by h.mon 35k • written 6.3 years ago by Phismil ▴ 20

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Which organism? Ploidity? For bacteria I usually use SPAdes.

ADD REPLY • link 6.3 years ago by Asaf 10k

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Thanks Asaf ! It is for mammalian genome (2n)!

ADD REPLY • link 6.3 years ago by Phismil ▴ 20

score 1 · Answer 1 · 2018-02-14

Do you have long range mate-pairs? Long reads? What is the genome size? What is the target coverage you have? What are the downstream analyses you ant to perform?

If you only have paired-end 2x250bp reads and no mate pairs, your draft assembly will be really fragmented, regardless of the assembler. For quick and dirty eukaryote assemblies, I have used Minia and MEGAHIT, with good results for my purposes.