table of contents
- bookworm 1.6.2+ds-3
- bookworm-backports 1.6.5+ds-2~bpo12+1
- testing 1.6.5+ds-2.2
- unstable 1.6.5+ds-2.2
GT-GENOMEDIFF(1) | GenomeTools Manual | GT-GENOMEDIFF(1) |
NAME¶
gt-genomediff - Calculates Kr: pairwise distances between genomes.
SYNOPSIS¶
gt genomediff [option ...] (INDEX | -indexname NAME SEQFILE SEQFILE [...])
DESCRIPTION¶
-indextype [...]
-indexname [string]
-unitfile [filename]
-mirrored [yes|no]
-pl [value]
-dc [value]
-memlimit [string]
-scan [yes|no]
-thr [value]
-abs_err [value]
-rel_err [value]
-M [value]
-v [yes|no]
-help
-help+
-version
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 (in Lua syntax):
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 in Lua start with -- and will be ignored.
See GTDIR/testdata/genomediff/unitfile1.lua for an example.
Options -pl, -dc and -memlimit are options to influence ESA construction.
REPORTING BUGS¶
Report bugs to <willrodt@zbh.uni-hamburg.de>.
04/27/2024 | GenomeTools 1.6.5 |