BOWTIE2(1) | User Commands | BOWTIE2(1) |
bowtie2 - wrapper for bowtie2-align-*
Bowtie 2 version 2.3.4.3 by Ben Langmead (langmea@cs.jhu.edu, www.cs.jhu.edu/~langmea)
bowtie2 [options]* -x <bt2-idx> {-1 <m1> -2 <m2> | -U <r> | --interleaved <i>} [-S <sam>]
Same as:
--very-fast -D 5 -R 1 -N 0 -L 22 -i S,0,2.50
--fast -D 10 -R 2 -N 0 -L 22 -i S,0,2.50
--sensitive -D 15 -R 2 -N 0 -L 22 -i S,1,1.15 (default)
--very-sensitive -D 20 -R 3 -N 0 -L 20 -i S,1,0.50
--very-fast-local -D 5 -R 1 -N 0 -L 25 -i S,1,2.00
--fast-local -D 10 -R 2 -N 0 -L 22 -i S,1,1.75
--sensitive-local -D 15 -R 2 -N 0 -L 20 -i S,1,0.75 (default)
--very-sensitive-local -D 20 -R 3 -N 0 -L 20 -i S,1,0.50
--fr/--rf/--ff -1, -2 mates align fw/rev, rev/fw, fw/fw (--fr)
--soft-clipped-unmapped-tlen Exclude soft-clipped bases when reporting TLEN
-p/--threads <int> number of alignment threads to launch (1)
--non-deterministic seed rand. gen. arbitrarily instead of using read attributes
September 2018 | bowtie2 2.3.4.3 |