DOKK / manpages / debian 10 / hilive / hilive.1.en
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

Print this help message and exit
Print licensing information and exit

Temporary directory for the alignment files [Default: use BaseCalls directory]
Create SAM files for each tile. [Default: no SAM files]
Keep intermediate alignment files [Default: false]
Select lane [Default: all lanes]
Select tile numbers [Default: all tiles]

Number of errors tolerated in read alignment
Report only the best alignmnet(s) for each read
Report the N best alignmnets for each read
Disable the One-Hit Wonder filter
First cycle to apply One-Hit Wonder filter
Set the window size to search for alignment continuation, i.e. maximum insertion/deletion size
Minimum allowed basecall quality

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
Compress alignment files. 0: no compression (default) 1: Deflate (smaller) 2: LZ4 (faster)
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