blasr(1) on Linux
The text 69ee7f326ec4, as Debian 9 (Stretch) shipped it.
Map SMRT Sequences to a reference genome.
Flags it lists
-
-affineAlign -
-aggressiveIntervalCut -
-allowAdjacentIndels -
-cigarUseSeqMatch -
-concordant -
-concordantTemplate -
-fastMaxInterval -
-fastSDP -
-h -
-header -
-hitPolicy -
-ignoreHQRegions -
-ignoreRegions -
-minAlnLength -
-minPctAccuracy -
-noSortRefinedAlignments -
-noSplitSubreads -
-placeRepeatsRandomly -
-printSAMQV -
-randomSeed -
-sam -
-subsample -
-useQuality -
-useccs -
-useccsall -
-useccsdenovo