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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.
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.