meta-velvet returns nodes instead of contigs in assembly?

deprekate · 10-24-2012, 06:50 PM

Hi I just started using meta-velvet to assemble a small metagenome 100k. The average length of reads are 102, with a min of 29 and a max of 227. I tried running meta-velvet with a k-mer of 21.

After the assembly is finished and I look at the output file "meta-velvetg.contigs.fa" I noticed that there are contigs of length 21 (less then the smallest read). This behavior seems strange, that it is returning just the k-mer overlap (or node) and the rest of the reads did not match, and shouldn't be reported as a contig

cliffbeall · 10-25-2012, 12:41 PM

I am not sure if this applies to meta-velvet, I only have used the original. However, with standard velvet, it reports the contig lengths in kmers rather than nt in the fasta headers. So is it possible that you have contigs with 21 kmers, that are actually 41 nt long?

deprekate · 10-25-2012, 02:53 PM

Ah, yes you are correct. The length of the actual sequence is >41 even though the header says length_21.

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10-24-2012, 06:50 PM	#1
deprekate Junior Member Location: San Diego Join Date: Oct 2012 Posts: 4	meta-velvet returns nodes instead of contigs in assembly? Hi I just started using meta-velvet to assemble a small metagenome 100k. The average length of reads are 102, with a min of 29 and a max of 227. I tried running meta-velvet with a k-mer of 21. After the assembly is finished and I look at the output file "meta-velvetg.contigs.fa" I noticed that there are contigs of length 21 (less then the smallest read). This behavior seems strange, that it is returning just the k-mer overlap (or node) and the rest of the reads did not match, and shouldn't be reported as a contig

10-25-2012, 02:53 PM	#3
deprekate Junior Member Location: San Diego Join Date: Oct 2012 Posts: 4	Ah, yes you are correct. The length of the actual sequence is >41 even though the header says length_21. Last edited by deprekate; 10-25-2012 at 04:59 PM.

10-25-2012, 12:41 PM	#2
cliffbeall Senior Member Location: Ohio Join Date: Jan 2010 Posts: 144	I am not sure if this applies to meta-velvet, I only have used the original. However, with standard velvet, it reports the contig lengths in kmers rather than nt in the fasta headers. So is it possible that you have contigs with 21 kmers, that are actually 41 nt long?