hisat2-align-l(1) on Linux
The text fe1ce22c31e6, as Debian 10 (Buster) shipped it.
HISAT2 graph-based alignment of short nucleotide reads to many genomes, large index binary
Flags it lists
-
--add-chrname -
--avoid-pseudogene -
--dta -
--dta-cufflinks -
--ignore-quals -
--int-quals -
--known-splicesite-infile -
--max-intronlen -
--met -
--met-file -
--met-stderr -
--min-intronlen -
--mm -
--mp -
--n-ceil -
--new-summary -
--no-discordant -
--no-head -
--no-mixed -
--no-softclip -
--no-spliced-alignment -
--no-sq -
--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 -
--quiet -
--rdg -
--remove-chrname -
--reorder -
--rfg -
--rg -
--rg-id -
--rna-strandness -
--seed -
--sp -
--summary-file -
--tmo -
--version -
-c -
-f -
-q -
-r