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Old 03-17-2011, 09:16 AM   #1
aloliveira
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Default 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
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Old 09-25-2012, 06:14 PM   #2
Torst
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Quote:
Originally Posted by aloliveira View Post
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)
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Old 09-26-2012, 11:19 PM   #3
A_Morozov
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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.
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Old 09-27-2012, 04:52 PM   #4
Torst
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Originally Posted by A_Morozov View Post
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.
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Old 09-28-2012, 12:43 AM   #5
boetsie
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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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