Hello,
I've used Bowtie2 to align 20 very short sequences (20nt) on a 100MB sequence while allowing 3 differences (either indels or substitutions). It took days (literally).
I've used this command line:
Is there anything to improve in order to have all the results with three differences but more quickly? (apart from running on several threads, obviously).
Thanks!
I've used Bowtie2 to align 20 very short sequences (20nt) on a 100MB sequence while allowing 3 differences (either indels or substitutions). It took days (literally).
I've used this command line:
Code:
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
Thanks!