recommendations for DeNovo assembly of short reads

Question

[Phismil]

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

[Asaf]

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

[Phismil]

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

Answer 1

[h.mon]

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.