NAME

       hilive - Realtime Alignment of Illumina Reads

SYNOPSIS

       hilive [options] BC_DIR INDEX CYCLES

DESCRIPTION

       HiLive  v0.1  -  Realtime  Alignment of Illumina Reads Copyright © 2015, Martin S. Lindner
       HiLive is open-source software. Check with --license for details.

       Fixed k-mer size: 15

       BC_DIR Illumina BaseCalls directory of the sequencing run to analyze

       INDEX  Path to k-mer index file (*.kix)

       CYCLES Total number of cycles for read 1

   General:
       -h [ --help ]
              Print this help message and exit

       --license
              Print licensing information and exit

   IO settings:
       --temp arg
              Temporary directory for the alignment files [Default: use BaseCalls directory]

       -S [ --sam ] arg
              Create SAM files for each tile. [Default: no SAM files]

       -k [ --keep-files ]
              Keep intermediate alignment files [Default: false]

       -l [ --lanes ] arg
              Select lane [Default: all lanes]

       -t [ --tiles ] arg
              Select tile numbers [Default: all tiles]

   Alignment settings:
       -e [ --min-errors ] arg (=2)
              Number of errors tolerated in read alignment

       -H [ --best-hit ]
              Report only the best alignmnet(s) for each read

       -N [ --best-n ] arg (=2)
              Report the N best alignmnets for each read

       --disable-ohw-filter
              Disable the One-Hit Wonder filter

       --start-ohw arg (=20)
              First cycle to apply One-Hit Wonder filter

       -w [ --window ] arg (=5)
              Set  the  window  size  to  search  for  alignment   continuation,   i.e.   maximum
              insertion/deletion size

       --min-quality arg (=1)
              Minimum allowed basecall quality

   Technical settings:
       --block-size arg
              Block  size for the alignment input/output stream in Bytes. Use -K or -M to specify
              in Kilobytes or Megabytes

       -K     Interpret the block-size argument as Kilobytes instead of Bytes

       -M     Interpret the block-size argument as Megabytes instead of Bytes

       -c [ --compression ] arg (=2)
              Compress alignment files. 0: no compression (default) 1: Deflate (smaller)  2:  LZ4
              (faster)

       -n [ --num-threads ] arg (=1)
              Number of threads to spawn

AUTHOR

       This  manpage was written by Andreas Tille for the Debian distribution and can be used for
       any other usage of the program.