Hai
I would like to assemble my metagenomes using MetaVelvet. I am planning to use VelvetOptimiser to determine the optimal K mer length first, then the determined K mer length will be used in my MetaVelvet assembly.
From my reading, the maximum K mer length for the VelvetOptimiser is 100, whereas the maximum K mer length can be used in MetaVelvet is 63.
Thus, I have to try several K mer length lesser than 63 in VelvetOptimiser right ? So that optimal K mer length could be used in MetaVelvet. Please correct me if I was wrong.
Secondly, may I assume that the number of nodes stated in the output file of VelvetOptimser is equal to number of contigs ? And when I proceed the assembly using MetaVelvet, I may assume that the number of nodes in the metavelvetg.LastGraph-stats.txt is equal to number of scaffolds of my metagenomes ?. What I had understood was MetaVelvet could reconstruct relatively low-overage genome sequences as scaffolds.
Lastly, do you mind to share any command line to calculate the length of N50 from my metavelvetg.LastGraph-stats.txt in linux perhaps or R statistical package ?. Looking forward for your response.
Thank You
I would like to assemble my metagenomes using MetaVelvet. I am planning to use VelvetOptimiser to determine the optimal K mer length first, then the determined K mer length will be used in my MetaVelvet assembly.
From my reading, the maximum K mer length for the VelvetOptimiser is 100, whereas the maximum K mer length can be used in MetaVelvet is 63.
Thus, I have to try several K mer length lesser than 63 in VelvetOptimiser right ? So that optimal K mer length could be used in MetaVelvet. Please correct me if I was wrong.
Secondly, may I assume that the number of nodes stated in the output file of VelvetOptimser is equal to number of contigs ? And when I proceed the assembly using MetaVelvet, I may assume that the number of nodes in the metavelvetg.LastGraph-stats.txt is equal to number of scaffolds of my metagenomes ?. What I had understood was MetaVelvet could reconstruct relatively low-overage genome sequences as scaffolds.
Lastly, do you mind to share any command line to calculate the length of N50 from my metavelvetg.LastGraph-stats.txt in linux perhaps or R statistical package ?. Looking forward for your response.
Thank You
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