Bowtie2 on very short sequences

[mikael]

Hello,

We have very short sequences (20nt) that we want to align with at most 3 errors (either indels or substitutions). We tried to use Bowtie2 for that purpose but it's taking days (literally) on 20 sequences.

Here is the command line used

bowtie2 -a --norc  -f -L 5 --mp 2 --rdg 0,2 --rfg 0,2 --score-min C,-6,0 -i C,5,0  --gbar 1  -x index -U sequences.fasta

(and we need the -a option)

Or maybe there are softwares that would be more suitable? (we also considered Razers3, MicroRazers)