Starting with beta 7, it seems Bowtie2 analyses take a lot longer to complete; for example to screen three files representing 3.15GB of gz compressed data, it takes:
- v2.0.0-b6: 219 seconds
- v2.0.0-b7 to 220.127.116.11: 294 seconds
The command line I used to run these analyses is:
bowtie2 --local -k 1 -N 1 -L 20 -i S,1,0.75 --ignore-quals --ma 4 --mp 12,12 --score-min G,-20,34 -x Ref -U data -p 6 -t --no-unal -S file.sam
Is this a bug or is this to be expected given some of the changes made in beta 7?