minimap2(1) on Linux
The text d25db1f18abb, as Debian 12 (Bookworm) shipped it.
mapping and alignment between collections of DNA sequences
Flags it lists
-
--MD -
--cs -
--dual -
--eqx -
--for-only -
--frag -
--hard-mask-level -
--heap-sort -
--idx-no-seq -
--junc-bed -
--junc-bonus -
--no-end-flt -
--no-hash-name -
--no-kalloc -
--no-long-join -
--no-pairing -
--paf-no-hit -
--print-qname -
--print-seeds -
--rev-only -
--rmq -
--sam-hit-only -
--secondary -
--splice -
--splice-flank -
--sr -
--version -
-2 -
-D -
-H -
-L -
-P -
-Q -
-X -
-Y -
-a -
-c -
-y