Scroll to navigation
HILIVE(1) |
User Commands |
HILIVE(1) |
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.