View Single Post
Old 09-28-2012, 01:43 AM   #5
boetsie
Senior Member
 
Location: NL, Leiden

Join Date: Feb 2010
Posts: 245
Default

Have you looked at the final contig and see which part is missing? Does any of your other four sequences contain a nearly similar sequence (e.g. one bp difference) than the missing part. Velvet uses k-mers (provided by the option 'hash_length' with velveth), if you have a k-mer that is near identical, the assembler does not know which path to choose. Example;

GATAGAGTAGAGA
GATAGAGTAGAGT

The assembler does not know if it should choose the A or T here. Look at the last x bases (where x depends on the set k-mer) of your contig, and see if any of the other four reads contains this k-mer.

Regards,
Boetsie
boetsie is offline   Reply With Quote