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