I am trying to do a short-long read hybrid de novo assembly on the MiSeq 2x75 paired end data and TruSeq long reads data (1500-16608bp) using three different assemblers, Velvet, ABySS, and SOAPdenovo.
I have already generated:
1) Velvet contigs using MiSeq only
2) ABySS contigs using MiSeq only
3) SOAP contigs using MiSeq only
And then, I combined the contigs with the long reads. For example,
cat Velvet_67/contigs.fa LongRead.fasta > Velvet_Hybrid.fasta
Now, I want to run assemblies using the hybrid fasta and three assemblers mentioned above.
My question is, how do I select the k-mer size?
For example, my Velvet_Hybrid.fasta has min read length of 133 and max read length of 16608.