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DISTANCEEST(1) User Commands DISTANCEEST(1)

NAME

DistanceEst - Estimate distances between contigs using paired-end alignments.

SYNOPSIS

DistanceEst -k<kmer> -s<seed-length> -n<npairs> [OPTION]... HIST [PAIR]

DESCRIPTION

Estimate distances between contigs using paired-end alignments.
Arguments:
HIST
distribution of fragments size
PAIR
alignments between contigs
Options:
--mind=N
minimum distance between contigs [-(k-1)]
--maxd=N
maximum distance between contigs
--fr
force the orientation to forward-reverse
--rf
force the orientation to reverse-forward
-k, --kmer=N
set --mind to -(k-1) bp
-l, --min-align=N
the minimal alignment size [1]
-n, --npairs=NPAIRS
minimum number of pairs
-s, --seed-length=L
minimum length of the seed contigs
-q, --min-mapq=N
ignore alignments with mapping quality less than this threshold [10]
-o, --out=FILE
write result to FILE
--mle
use the MLE [default] (maximum likelihood estimator)
--median
use the difference of the population median and the sample median
--mean
use the difference of the population mean and the sample mean
--dist
output the graph in dist format [default]
--dot
output the graph in GraphViz format
--gv
output the graph in GraphViz format
--gfa
output the graph in GFA2 format
--gfa2
output the graph in GFA2 format
-j, --threads=N
use N parallel threads [1]
-v, --verbose
display verbose output
--help
display this help and exit
--version
output version information and exit
--db=FILE
specify path of database repository in FILE
--library=NAME
specify library NAME for sqlite
--strain=NAME
specify strain NAME for sqlite
--species=NAME
specify species NAME for sqlite

AUTHOR

Written by Jared Simpson and Shaun Jackman.

REPORTING BUGS

Report bugs to <abyss-users@bcgsc.ca>.

COPYRIGHT

Copyright 2014 Canada's Michael Smith Genome Sciences Centre
September 2019 DistanceEst (ABySS) 2.2.3