AdapterRemoval(1) on Linux
The text 2580953726cd, as Debian 12 (Bookworm) shipped it.
Fast short-read adapter trimming and processing
Flags it lists
-
--adapter-list -
--adapter1 -
--adapter2 -
--barcode-list -
--barcode-mm -
--barcode-mm-r1 -
--barcode-mm-r2 -
--basename -
--bzip2 -
--bzip2-level -
--collapse -
--collapse-conservatively -
--collapse-deterministic -
--combined-output -
--demultiplex-only -
--discarded -
--gzip -
--gzip-level -
--help -
--identify-adapters -
--interleaved -
--interleaved-input -
--interleaved-ouput -
--mate-separator -
--maxlength -
--maxns -
--minadapteroverlap -
--minalignmentlength -
--minlength -
--minquality -
--mm -
--output1 -
--output2 -
--outputcollapsed -
--outputcollapsedtruncated -
--preserve5p -
--qualitybase -
--qualitybase-output -
--qualitymax -
--seed -
--settings -
--shift -
--singleton -
--threads -
--trimns -
--trimqualities -
--trimwindows -
--version