hilive(1) on Linux
The text 0f39811dab3b, as Debian 12 (Bookworm), Debian 11 (Bullseye) shipped it. The page shows this text now.
Realtime Alignment of Illumina Reads
Flags it lists
-
--align-undetermined-barcodes -
--anchor-length -
--barcode-errors -
--block-size -
--compression -
--continue -
--deletion-extension-penalty -
--deletion-opening-penalty -
--error-interval -
--extended-cigar -
--flowcell-id -
--force-resort -
--help -
--insertion-opening-penalty -
--instrument-id -
--keep-all-files -
--keep-invalid-sequences -
--license -
--match-score -
--max-gap-length -
--max-softclip-length -
--max-softclip-ratio -
--min-basecall-quality -
--mismatch-penalty -
--report-unmapped -
--run-id -
--runinfo -
--seeding-interval -
--softclip-extension-penalty -
--softclip-opening-penalty -
--temp-dir -
-K -
-b -
-h -
-i -
-l -
-r