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