tophat(1) on Linux
The text 30e961fface6, as Debian 8 (Jessie) shipped it.
TopHat maps short sequences from spliced transcripts to whole genomes
Flags it lists
-
--b2-D -
--b2-L -
--b2-N -
--b2-R -
--b2-gbar -
--b2-i -
--b2-mp -
--b2-n-ceil -
--b2-np -
--b2-rdg -
--b2-rfg -
--b2-score-min -
--bowtie-n -
--bowtie1 -
--deletions -
--fusion-anchor-length -
--fusion-do-not-resolve-conflicts -
--fusion-ignore-chromosomes -
--fusion-min-dist -
--fusion-multipairs -
--fusion-multireads -
--fusion-read-mismatches -
--insertions -
--library-type -
--mate-std-dev -
--max-coverage-intron -
--max-deletion-length -
--max-insertion-length -
--max-segment-intron -
--min-coverage-intron -
--min-segment-intron -
--no-convert-bam -
--no-sort-bam -
--phred64-quals -
--read-edit-dist -
--read-gap-length -
--read-realign-edit-dist -
--rg-center -
--rg-date -
--rg-description -
--rg-id -
--rg-library -
--rg-platform -
--rg-platform-unit -
--rg-sample -
--segment-length -
--segment-mismatches -
--solexa1.3-quals -
--tmp-dir -
--transcriptome-index