bowtie2-align-l(1) on Linux
The text 9dda8d42aedc, as Debian 8 (Jessie) shipped it.
ultrafast and memory-efficient backend tool for aligning sequencing reads to long reference sequences
Flags it lists
-
--dpad -
--end-to-end -
--gbar -
--ignore-quals -
--int-quals -
--local -
--ma -
--met -
--met-file -
--met-stderr -
--mm -
--mp -
--n-ceil -
--no-1mm-upfront -
--no-contain -
--no-discordant -
--no-dovetail -
--no-head -
--no-mixed -
--no-overlap -
--no-sq -
--no-unal -
--nofw -
--norc -
--np -
--omit-sec-seq -
--phred33 -
--phred64 -
--qc-filter -
--qseq -
--quiet -
--rdg -
--reorder -
--rfg -
--rg -
--rg-id -
--seed -
--version -
-D -
-L -
-N -
-R -
-c -
-f -
-i -
-k -
-q -
-r