DistanceEst - Estimate distances between contigs using paired-end
alignments.
DistanceEst -k<kmer> -s<seed-length>
-n<npairs> [OPTION]... HIST [PAIR]
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
Written by Jared Simpson and Shaun Jackman.
Report bugs to <abyss-users@bcgsc.ca>.
Copyright 2014 Canada's Michael Smith Genome Sciences Centre