I have previously used Velvet for paired end de Novo assembly of bacterial genomes using 36 base pair reads. We have now recieved some reads that are 72 base per long. Using Velvet on these data set result in a very large number of contigs (several thousands). When the sequences are cut down to 36 base the number of contigs become as expected (a few hundreds with a correct genome size). I have also tried to split the 72 bp in two 36 sets with good result (i.e it is not due to low quality at the ends). Anyone else had these problems with "long" Illumina reads and how did you deal with it?
I have used both Velvet 0.7.20 and 0.7.31.
Best regards,
Peter
I have used both Velvet 0.7.20 and 0.7.31.
Best regards,
Peter
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