.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.3.
.TH SURANKCO-SCORE "1" "March 2016" "surankco-score 0.0.r5" "User Commands"
.SH NAME
surankco-score \- alignment of contigs and reference genomes and score calculation
.SH SYNOPSIS
.B surankco-score
[\fI\,options\/\fR]
.SH DESCRIPTION
Alignment of contigs (FASTA format) and reference genomes (FASTA format) and score calculation
.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 (default "*.contigs.fasta")
.HP
\fB\-d\fR DIRECTORY, \fB\-\-directory\fR=\fI\,DIRECTORY\/\fR
.IP
Indicate a directory containing assembly files with indicated
format (e.g. "*.contigs.fasta")
.HP
\fB\-f\fR ASSEMBLY.SUFFIX, \fB\-\-assembly\fR.suffix=ASSEMBLY.SUFFIX
.IP
Indicate assembly format/suffix, default="contigs.fasta"
.HP
\fB\-r\fR REFERENCE.SUFFIX, \fB\-\-reference\fR.suffix=REFERENCE.SUFFIX
.IP
Indicate the reference format/suffix, default="ref.fasta"
.HP
\fB\-p\fR PDF.HISTOGRAMS, \fB\-\-pdf\fR.histograms=PDF.HISTOGRAMS
.IP
Indicate a name for the score histogram pdf
(default = "surankco_score_histograms.pdf")
.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\-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.