Illumina Hiseq 2000 Reads Assembly (Genomic Dna)

Question

[Rahul Sharma]

Hi,

I have Illumina HiSeq 2000 reads with ~100-140 read length (Genomic DNA). Which assembler is the best for this data assembly. I used velvet for 76bp read size, It will not work here, I think.

Thanks in advance, Rahul

[zam.iqbal.genome]

You'll get more productive replies from everyone if you give more information. Some of the information people might need to be able to help are: What genome size. What ploidy. What depth of coverage. What type of species. Why do you think velvet works for 76bp but not 100bp? Also, look up the Assemblathon 1 and 2 papers.

[Rahul Sharma]

HI,

Thanks!! By the way it was very quick question. I installed velvet with large k-mer size and it worked. Thanks

[zam.iqbal.genome]

OK - does that mean you are now happy and the question can be closed? cheers Zam

Answer 1

[Alastair Kerr]

This is probably a good place to highlight the assemblathon 2.