hisat2(1) on Linux
The text 5d4844f42e2c, as Debian 12 (Bookworm) shipped it.
graph-based alignment of short nucleotide reads to many genomes, wrapper script
Flags it lists
-
--add-chrname -
--al -
--al-conc -
--avoid-pseudogene -
--dta -
--dta-cufflinks -
--ignore-quals -
--int-quals -
--known-splicesite-infile -
--max-intronlen -
--max-seeds -
--min-intronlen -
--mm -
--mp -
--n-ceil -
--no-discordant -
--no-mixed -
--no-repeat-index -
--no-softclip -
--no-spliced-alignment -
--no-temp-splicesite -
--no-templatelen-adjustment -
--nofw -
--norc -
--novel-splicesite-infile -
--novel-splicesite-outfile -
--np -
--omit-sec-seq -
--pen-canintronlen -
--pen-cansplice -
--pen-noncanintronlen -
--pen-noncansplice -
--phred33 -
--phred64 -
--qc-filter -
--qseq -
--rdg -
--remove-chrname -
--reorder -
--repeat -
--rfg -
--rna-strandness -
--seed -
--sp -
--tmo -
--un -
--un-conc -
--version -
-c -
-f -
-k -
-q -
-r