Ive pair-end reads from papaya samples with average length of 151 bp. I used IDBA_UD for assembling. I increased the read length and kmer size by changing the default value as follows
static const uint32_t kMaxShortSequence = 200; static const uint32_t kNumUint64 = 16; ./idba_ud -r reads.fa -o output mink 20 maxk 140
I have two questions.
- When I executed IDBA_UD, It gave the contigs for the kmer size 20-100 only. I did not get any contigs for the kmer more than 100. Where I have gone wrong?
- My second question is, The program internally decides the best kmer and produces the contig.fa file. How do we know which kmer is used to create this contig files?