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Old 01-30-2013, 11:55 PM   #1
hard998
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Location: beijing

Join Date: Jun 2009
Posts: 4
Default contig overlaps in velvet 1.2.03

Hi, I did a denovo assembly using velvet 1.2.03 which gave me 1626 contigs,

However, when I examined the contig.fa output by velvet, eg
>NODE_1331_length_2655_cov_63.920151
>NODE_1395_length_1978_cov_42.813953
...

I found 689 contigs have tail-to-tail matches with each other by doing BLAST, such as
NODE_1331_length_2655_cov_63.920151: 2656 tgcggctggtcggctcgtcgcaggcgaacatgttcgcctccatc 2699
||||||||||||||||||||||||||||||||||||||||||||
NODE_1395_length_1978_cov_42.813953: 2022 tgcggctggtcggctcgtcgcaggcgaacatgttcgcctccatc 1979


Can anyone tell me why didn't velvet merge those overlaps? Is that correct for me to join contigs into larger contigs? Thank you!
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Old 02-04-2013, 08:52 PM   #2
seb567
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Location: Québec, Canada

Join Date: Jul 2008
Posts: 256
Default

Quote:
Originally Posted by hard998 View Post
Hi, I did a denovo assembly using velvet 1.2.03 which gave me 1626 contigs,

However, when I examined the contig.fa output by velvet, eg
>NODE_1331_length_2655_cov_63.920151
>NODE_1395_length_1978_cov_42.813953
...

I found 689 contigs have tail-to-tail matches with each other by doing BLAST, such as
NODE_1331_length_2655_cov_63.920151: 2656 tgcggctggtcggctcgtcgcaggcgaacatgttcgcctccatc 2699
||||||||||||||||||||||||||||||||||||||||||||
NODE_1395_length_1978_cov_42.813953: 2022 tgcggctggtcggctcgtcgcaggcgaacatgttcgcctccatc 1979


Can anyone tell me why didn't velvet merge those overlaps? Is that correct for me to join contigs into larger contigs? Thank you!
These are called repeats. You probably have more than 2 contigs with this sequence on one end. Therefore, Velvet did not merge them because that would cause an assembly error, which produce chimeric contigs.
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