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Old 03-27-2015, 04:41 AM   #1
bio_informatics
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Default SPAdes: does contig with node id has/refer coverage?

Hi Members,
I'm working on bacteria genome, illumina Hiseq paired end reads.
Used:
- trimmomatic with illumina adapter file.
- spades for assembly with careful flag, bayes hammer correction.

I get 2 fasta files: contigs and scaffolds.
Contigs and scaffolds file give output in below fashion:

scaffolds-
Quote:
>NODE_452_length_82_cov_291.815_ID_903
contigs-
Quote:
>NODE_488_length_109_cov_1.07407_ID_975
My question:
Does cov_1.07407 and cov_291.815 refer to coverage of the contig/scaffold?

Thank you.
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Old 03-27-2015, 05:24 AM   #2
akorobeynikov
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Yes, like in Velvet, this is the average k-mer coverage of a contig/scaffold. Use the last k-mer length if you need to convert to read coverage.
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Old 03-27-2015, 05:29 AM   #3
bio_informatics
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Hi,
Thanks for your reply.
I do not quite understand what you meant. I have not really well read/understood on Velvet. (Have basic knowledge that it works on de bruijn graphs and so so..)

Quote:
Originally Posted by akorobeynikov View Post
Yes, like in Velvet, this is the average k-mer coverage of a contig/scaffold. Use the last k-mer length if you need to convert to read coverage.
My assembly ran on 21, 33 and 55 k-mer (default SPAdes run).
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Old 03-27-2015, 05:32 AM   #4
akorobeynikov
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Quote:
Originally Posted by bio_informatics View Post
Hi,
Thanks for your reply.
I do not quite understand what you meant. I have not really well read/understood on Velvet. (Have basic knowledge that it works on de bruijn graphs and so so..)



My assembly ran on 21, 33 and 55 k-mer (default SPAdes run).
Check this http://seqanswers.com/forums/showthread.php?t=1529 for k-mer coverage. Use k=55 for SPAdes in this case.
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Old 03-27-2015, 05:44 AM   #5
bio_informatics
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Thank you for directing to that page.

Indeed the below URL far better explains what I was looking for:

http://seqanswers.com/forums/showthread.php?t=6887

Merci!
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