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Illumina Hiseq 2000 Reads Assembly (Genomic Dna)

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

illumina hiseq genome assembly
• 4,254 views • link
updated by Alastair Kerr Alastair Kerr • written by Rahul Sharma Rahul Sharma

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.

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written by zam.iqbal.genome zam.iqbal.genome

HI,

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

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written by Rahul Sharma Rahul Sharma

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

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written by zam.iqbal.genome zam.iqbal.genome

1 answer

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

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updated by Ram Ram • written by Alastair Kerr Alastair Kerr

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