BOWTIE2-ALIGN-L(1) | User Commands | BOWTIE2-ALIGN-L(1) |
bowtie2-align-l - ultrafast and memory-efficient backend tool for aligning sequencing reads to long reference sequences
Bowtie 2 version 2.5.0 by Ben Langmead (langmea@cs.jhu.edu, www.cs.jhu.edu/~langmea)
bowtie2-align [options]* -x <bt2-idx> {-1 <m1> -2 <m2> | -U <r> | --interleaved <i> | -b <bam>} [-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)
-p/--threads <int> number of alignment threads to launch (1)
February 2023 | bowtie2-align-l 2.5.0 |