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Hi
I have a metagenomic dataset composed by ~300 Million pair end reads (HiSeq) 150 bp read length and ~380 average fragment size.
I'm trying to run meta-velvet to assemble metagenomes. After choosing a kmer size of either 51 or 75 I see no difference between outputs from velvetg and meta-velvetg.
Furthermore, after running EstimateCovMulti.py, I end up with a -1 coverage peak value for both velvetg and meta-velvetg and the same very low N50 (~399). Strangely, that does not happen with all my samples.
Can anybody give me some clues as to what's going on here?
I'd really appreciate it
A
I have a metagenomic dataset composed by ~300 Million pair end reads (HiSeq) 150 bp read length and ~380 average fragment size.
I'm trying to run meta-velvet to assemble metagenomes. After choosing a kmer size of either 51 or 75 I see no difference between outputs from velvetg and meta-velvetg.
Furthermore, after running EstimateCovMulti.py, I end up with a -1 coverage peak value for both velvetg and meta-velvetg and the same very low N50 (~399). Strangely, that does not happen with all my samples.
Can anybody give me some clues as to what's going on here?
I'd really appreciate it
A