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-   -   How can be possible? (Velvet) (http://seqanswers.com/forums/showthread.php?t=10154)

aloliveira 03-17-2011 10:16 AM

How can be possible? (Velvet)
 
I provide 5 reads to velvet (one read with 600 bp in size and the other four with 70 bp). After running , velvet returns an assembly with one contig with 572 bp in size. How can be possible an assembler returns a contig smaller than one of the reads???

Best regards,
André

Torst 09-25-2012 07:14 PM

Quote:

Originally Posted by aloliveira (Post 37406)
I provide 5 reads to velvet (one read with 600 bp in size and the other four with 70 bp). After running , velvet returns an assembly with one contig with 572 bp in size. How can be possible an assembler returns a contig smaller than one of the reads???

What was the command line you used to run Velvet?

(It's an artifact of your low coverage, and edge-effects of k-mers)

A_Morozov 09-27-2012 12:19 AM

May I ask a noobish question? Is it 5 reads as in "Five pieces of DNA sequence being read by some method" and if yes, how did you end up assembling it? No insult meant, I'm really curious.

Torst 09-27-2012 05:52 PM

Quote:

Originally Posted by A_Morozov (Post 85028)
May I ask a noobish question? Is it 5 reads as in "Five pieces of DNA sequence being read by some method" and if yes, how did you end up assembling it? No insult meant, I'm really curious.

I think the user is just testing Velvet, and is wondering why, if they feed it 5 sequences, one of which is 600bp, why do they get a final contig out that is shorter than 600bp. ie. what happened to the other 28bp.

boetsie 09-28-2012 01:43 AM

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


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