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Old 04-02-2012, 01:39 AM   #1
sarbashis
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Location: India

Join Date: Jun 2010
Posts: 17
Default soapdenovo singletons??

I did a denovo assembly of bacteria genome using soapdenvo. I got lots of singletons. I found these singletons are generally repeat sequences. Is there any way to connect these singletons with the scaffolds ?
Another questions, when I realigned reads with soap2 I found most paired-end reads are out of average insert size ? Does this affect the assembly? I tried with different kmer and chosen kmer with hightest N50 and N90. If any one guide me, I will be thankful.
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