GT-GENOMEDIFF(1)

NAME
gt-genomediff - Calculates Kr: pairwise distances between genomes.

SYNOPSIS

gt genomediff [option ...] (INDEX | -indexname NAME SEQFILE SEQFILE [...])

OPTIONS

-indextype
    specify type of index, one of: esa|pck|encseq. Where encseq is an encoded sequence and an enhanced suffix array will be constructed only in memory. (default: encseq)

-indexname
    Basename of encseq to construct. (default: undefined)

-unitfile
    specifies genomic units, see below for description. (default: undefined)

-mirrored
    virtually append the reverse complement of each sequence (default: no)

-pl
    specify prefix length for bucket sort recommendation: use without argument; then a reasonable prefix length is automatically determined. (default: 0)

-dc
    specify difference cover value (default: 0)

-memlimit
    specify maximal amount of memory to be used during index construction (in bytes, the keywords MB and GB are allowed) (default: undefined)

-v
    be verbose (default: no)

-help
    display help for basic options and exit

-help+
    display help for all options and exit

-version
    display version information and exit

DESCRIPTION

The genomediff tool only accepts DNA input.

When used with sequence files or encseq, an enhanced suffix array will be built in memory. The ESA will not be created completely, but construction will use -memlimit as a threshold and build it partwise, calculating the Shu-length for each part.

File format for option -unitfile (lua):

    units = {
     genome1 = { "path/file1.fa", "file2.fa" },
     genome2 = { "file3.fa", "path/file4.fa" }
    }

Give the path to the files as they were given to the encseq tool! You can use gt encseq info INDEXNAME to get a list of files in an encoded sequence.

Comment lines start with -- and will be ignored. See GTDIR/testdata/genomediff/unitfile1.lua for an example.

Options -pl -dc -memlimit are options to influence esa construction.

AUTHOR

Report bugs to <willrodt@zbh.uni-hamburg.de>.