.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.4.
.TH HILIVE "1" "July 2016" "hilive 0.0+20150926" "User Commands"
.SH NAME
hilive \- Realtime Alignment of Illumina Reads
.SH SYNOPSIS
.B hilive
[\fI\,options\/\fR] \fI\,BC_DIR INDEX CYCLES\/\fR
.SH DESCRIPTION
HiLive v0.1 \- Realtime Alignment of Illumina Reads
Copyright \(co 2015, Martin S. Lindner
HiLive is open\-source software. Check with \fB\-\-license\fR for details.
.PP
Fixed k\-mer size: 15
.TP
BC_DIR
Illumina BaseCalls directory of the sequencing run to analyze
.TP
INDEX
Path to k\-mer index file (*.kix)
.TP
CYCLES
Total number of cycles for read 1
.SS "General:"
.TP
\fB\-h\fR [ \fB\-\-help\fR ]
Print this help message and exit
.TP
\fB\-\-license\fR
Print licensing information and exit
.SS "IO settings:"
.TP
\fB\-\-temp\fR arg
Temporary directory for the alignment files
[Default: use BaseCalls directory]
.TP
\fB\-S\fR [ \fB\-\-sam\fR ] arg
Create SAM files for each tile. [Default: no
SAM files]
.TP
\fB\-k\fR [ \fB\-\-keep\-files\fR ]
Keep intermediate alignment files [Default:
false]
.TP
\fB\-l\fR [ \fB\-\-lanes\fR ] arg
Select lane [Default: all lanes]
.TP
\fB\-t\fR [ \fB\-\-tiles\fR ] arg
Select tile numbers [Default: all tiles]
.SS "Alignment settings:"
.TP
\fB\-e\fR [ \fB\-\-min\-errors\fR ] arg (=2)
Number of errors tolerated in read alignment
.TP
\fB\-H\fR [ \fB\-\-best\-hit\fR ]
Report only the best alignmnet(s) for each
read
.TP
\fB\-N\fR [ \fB\-\-best\-n\fR ] arg (=2)
Report the N best alignmnets for each read
.TP
\fB\-\-disable\-ohw\-filter\fR
Disable the One\-Hit Wonder filter
.TP
\fB\-\-start\-ohw\fR arg (=20)
First cycle to apply One\-Hit Wonder filter
.TP
\fB\-w\fR [ \fB\-\-window\fR ] arg (=5)
Set the window size to search for alignment
continuation, i.e. maximum insertion/deletion
size
.TP
\fB\-\-min\-quality\fR arg (=1)
Minimum allowed basecall quality
.SS "Technical settings:"
.TP
\fB\-\-block\-size\fR arg
Block size for the alignment input/output
stream in Bytes. Use \fB\-K\fR or \fB\-M\fR to specify in
Kilobytes or Megabytes
.TP
\fB\-K\fR
Interpret the block\-size argument as Kilobytes
instead of Bytes
.TP
\fB\-M\fR
Interpret the block\-size argument as Megabytes
instead of Bytes
.TP
\fB\-c\fR [ \fB\-\-compression\fR ] arg (=2)
Compress alignment files. 0: no compression
(default) 1: Deflate (smaller) 2: LZ4 (faster)
.TP
\fB\-n\fR [ \fB\-\-num\-threads\fR ] arg (=1)
Number of threads to spawn
.SH AUTHOR
This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.