Man page - distanceest(1)

Packages contains this manual

Package: abyss
apt-get install abyss

Manuals in package:

Documentations in package:

abyss

Manual

DISTANCEEST

NAME
SYNOPSIS
DESCRIPTION
AUTHOR
REPORTING BUGS
COPYRIGHT

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>.