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Old 01-25-2013, 07:43 AM   #1
Location: US

Join Date: Sep 2012
Posts: 91
Default Velveth flag question

I've been generating

velveth Assem1 85 -create_binary -shortPaired -fastq -separate
upon closer examination of the manual, it should be

velveth Assem2 85 -create_binary -fastq -shortPaired -separate
Amusingly, the results are different

Final graph has 4275 nodes and n50 of 11961, max 59442, total 4748899, using 12959473/18913301 reads
Final graph has 4229 nodes and n50 of 11829, max 57667, total 4724268, using 13243576/18913301 reads
Obviously I need to directly compare contigs and see what the real changes were from an assembly standpoint...but I wonder how velvet is interpreting the results for the first velveth input if it is isn't the same as the canonical, second version.

Reposting to the velveth mailing list.

Last edited by winsettz; 01-25-2013 at 07:48 AM.
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