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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:
distribution of fragments size
alignments between contigs
Options:
minimum distance between contigs [-(k-1)]
maximum distance between contigs
force the orientation to forward-reverse
force the orientation to reverse-forward
set --mind to -(k-1) bp
the minimal alignment size [1]
minimum number of pairs
minimum length of the seed contigs
ignore alignments with mapping quality less than this threshold [10]
write result to FILE
use the MLE [default] (maximum likelihood estimator)
use the difference of the population median and the sample median
use the difference of the population mean and the sample mean
output the graph in dist format [default]
output the graph in GraphViz format
output the graph in GraphViz format
output the graph in GFA2 format
output the graph in GFA2 format
use N parallel threads [1]
display verbose output
display this help and exit
output version information and exit
specify path of database repository in FILE
specify library NAME for sqlite
specify strain NAME for sqlite
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

November 2024 ABySS 2.3.10