.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.3.
.TH SURANKCO-FEATURE "1" "March 2016" "surankco-feature 0.0.r5" "User Commands"
.SH NAME
surankco-feature \- feature generation from contigs and corresponding reads
.SH SYNOPSIS
.B surankco-feature
[\fI\,options\/\fR]
.SH DESCRIPTION
Feature generation from contigs (ACE format) and corresponding reads (QUAL or FASTQ format).
.SH OPTIONS
.HP
\fB\-a\fR ASSEMBLIES, \fB\-\-assemblies\fR=\fI\,ASSEMBLIES\/\fR
.IP
Indicate a list of assembly files (comma separated), correct
suffixes are mandatory (e.g. ".ace")
.HP
\fB\-d\fR DIRECTORY, \fB\-\-directory\fR=\fI\,DIRECTORY\/\fR
.IP
Indicate a directory containing assembly files with indicated
format (default: ace, see parameter \fB\-f\fR)
.HP
\fB\-f\fR ASSEMBLY.FORMAT, \fB\-\-assembly\fR.format=ASSEMBLY.FORMAT
.IP
Indicate assembly/contig format (resp. suffix),
either "ace" (default) or "contigs.fasta"
.HP
\fB\-r\fR READ.QUALITY.FORMAT, \fB\-\-read\fR.quality.format=READ.QUALITY.FORMAT
.IP
Indicate the read quality format: qual, qua or fastq for ACE
(default="qual") resp. sam or bam for contigs.fasta (default="sam")
.HP
\fB\-q\fR FASTQ.VERSION, \fB\-\-fastq\fR.version=FASTQ.VERSION
.IP
Indicate the fastq version: auto, sanger, solexa, illumina13,
illumina15, illumina18 (default). Only needed for ACE assemblies.
.HP
\fB\-s\fR SPLIT.REGEX, \fB\-\-split\fR.regex=SPLIT.REGEX
.IP
Indicate a regular expression to cutoff read names (e.g. if
modified by the assembler). Only needed for ACE assemblies.
Note, if a backslash "\e" is needed use "\e\e\e\e"!
.HP
\fB\-t\fR THREADS, \fB\-\-threads\fR=\fI\,THREADS\/\fR
.IP
Indicate a number of cores or threads to use. Might speed up
some parallelized operations (default: 1)
.HP
\fB\-m\fR MEMORY, \fB\-\-memory\fR=\fI\,MEMORY\/\fR
.IP
Indicate the maximum memory usage (in Gb) of Javas virtual
machine (default: 32). Try to increase if big data sets report
heap space problems.
.HP
\fB\-k\fR, \fB\-\-kmer\fR.features
.IP
Indicates whether k\-mer features should be computed
(experimental, very long runtime) or not (default)
.HP
\fB\-g\fR EXPECTED.GENOME.SIZE, \fB\-\-expected\fR.genome.size=EXPECTED.GENOME.SIZE
.IP
Indicate a list of expected genome sizes (comma separated) or
one value for all assemblies. Default is 0, which will estimate
the genome sizes as sum of contig lengths.
.HP
\fB\-c\fR CONTIG.SIZE.FILTER, \fB\-\-contig\fR.size.filter=CONTIG.SIZE.FILTER
.IP
Indicate a minimum contig size. Default: 0
.HP
\fB\-h\fR, \fB\-\-help\fR
.IP
Show this help message and exit
.SH AUTHOR
This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.