.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.3.
.TH DISTANCEEST "1" "December 2023" "ABySS 2.3.7" "User Commands"
.SH NAME
DistanceEst \- Estimate distances between contigs using paired-end alignments.
.SH SYNOPSIS
.B DistanceEst
\fI\,-k<kmer> -s<seed-length> -n<npairs> \/\fR[\fI\,OPTION\/\fR]... \fI\,HIST \/\fR[\fI\,PAIR\/\fR]
.SH DESCRIPTION
Estimate distances between contigs using paired\-end alignments.
.IP
Arguments:
.TP
HIST
distribution of fragments size
.TP
PAIR
alignments between contigs
.IP
Options:
.TP
\fB\-\-mind\fR=\fI\,N\/\fR
minimum distance between contigs [\-(k\-1)]
.TP
\fB\-\-maxd\fR=\fI\,N\/\fR
maximum distance between contigs
.TP
\fB\-\-fr\fR
force the orientation to forward\-reverse
.TP
\fB\-\-rf\fR
force the orientation to reverse\-forward
.TP
\fB\-k\fR, \fB\-\-kmer\fR=\fI\,N\/\fR
set \fB\-\-mind\fR to \-(k\-1) bp
.TP
\fB\-l\fR, \fB\-\-min\-align\fR=\fI\,N\/\fR
the minimal alignment size [1]
.TP
\fB\-n\fR, \fB\-\-npairs\fR=\fI\,NPAIRS\/\fR
minimum number of pairs
.TP
\fB\-s\fR, \fB\-\-seed\-length\fR=\fI\,L\/\fR
minimum length of the seed contigs
.TP
\fB\-q\fR, \fB\-\-min\-mapq\fR=\fI\,N\/\fR
ignore alignments with mapping quality
less than this threshold [10]
.TP
\fB\-o\fR, \fB\-\-out\fR=\fI\,FILE\/\fR
write result to FILE
.TP
\fB\-\-mle\fR
use the MLE [default]
(maximum likelihood estimator)
.TP
\fB\-\-median\fR
use the difference of the population median
and the sample median
.TP
\fB\-\-mean\fR
use the difference of the population mean
and the sample mean
.TP
\fB\-\-dist\fR
output the graph in dist format [default]
.TP
\fB\-\-dot\fR
output the graph in GraphViz format
.TP
\fB\-\-gv\fR
output the graph in GraphViz format
.TP
\fB\-\-gfa\fR
output the graph in GFA2 format
.TP
\fB\-\-gfa2\fR
output the graph in GFA2 format
.TP
\fB\-j\fR, \fB\-\-threads\fR=\fI\,N\/\fR
use N parallel threads [1]
.TP
\fB\-v\fR, \fB\-\-verbose\fR
display verbose output
.TP
\fB\-\-help\fR
display this help and exit
.TP
\fB\-\-version\fR
output version information and exit
.TP
\fB\-\-db\fR=\fI\,FILE\/\fR
specify path of database repository in FILE
.TP
\fB\-\-library\fR=\fI\,NAME\/\fR
specify library NAME for sqlite
.TP
\fB\-\-strain\fR=\fI\,NAME\/\fR
specify strain NAME for sqlite
.TP
\fB\-\-species\fR=\fI\,NAME\/\fR
specify species NAME for sqlite
.SH AUTHOR
Written by Jared Simpson and Shaun Jackman.
.SH "REPORTING BUGS"
Report bugs to <abyss\-users@bcgsc.ca>.
.SH COPYRIGHT
Copyright 2014 Canada's Michael Smith Genome Sciences Centre