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Old 01-31-2012, 08:16 AM   #3
Retro
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Location: Pennsylvania

Join Date: Apr 2011
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Thanks for your response. The clusters should have a length of one read. They can contain for example 50 reads, but all reads start at position 1 ("left side" in aligned cluster). The reads in a cluster might differ in length based on the initial fragmentation.

To make it more difficult, our reads come from a pool of animals, so in addition to sequencing errors we also see SNPs. That is why we cannot use assembly based on let's say 99% homology. The de novo algorithm then starts adding read to our clusters that extend the cluster in length, mosty based on random inverted repeats in the genomic tags.
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