Hi ,
I'm looking for doing an assembly on a between 80 to 100Mb nematode genome.
I've paired end 2x250bp , and I read a lot about assembly on the internet but I confused me more than help me to choose the right tool ...
I read a lot on SPAdes, velvet, soapdenovo, abyss, ... The problem is that the kmer size is really short , and I read that I've to take a kmer size of more than the half mean length sequence, and preferrably 2/3 of the mean length sequence, normally it's 146 here. But I can do it with no one.
Have you solutions for me, or way to continue my research ?
Regards
PacMan
I'm looking for doing an assembly on a between 80 to 100Mb nematode genome.
I've paired end 2x250bp , and I read a lot about assembly on the internet but I confused me more than help me to choose the right tool ...
I read a lot on SPAdes, velvet, soapdenovo, abyss, ... The problem is that the kmer size is really short , and I read that I've to take a kmer size of more than the half mean length sequence, and preferrably 2/3 of the mean length sequence, normally it's 146 here. But I can do it with no one.
Have you solutions for me, or way to continue my research ?
Regards
PacMan
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