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HILIVE(1) User Commands HILIVE(1)


hilive - Realtime Alignment of Illumina Reads


hilive [options] BC_DIR INDEX CYCLES


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

Illumina BaseCalls directory of the sequencing run to analyze
Path to k-mer index file (*.kix)
Total number of cycles for read 1


-h [ --help ]
Print this help message and exit
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 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
Interpret the block-size argument as Kilobytes instead of Bytes
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


This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
July 2016 hilive 0.0+20150926