How can be possible? (Velvet)

aloliveira · 03-17-2011, 10:16 AM

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

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

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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03-17-2011, 10:16 AM	#1
aloliveira Member Location: Brazil Join Date: Aug 2010 Posts: 47	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

09-27-2012, 12:19 AM	#3
A_Morozov Member Location: Russia, Irkutsk Join Date: Feb 2011 Posts: 40	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.

09-28-2012, 01:43 AM	#5
boetsie Senior Member Location: NL, Leiden Join Date: Feb 2010 Posts: 245	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