GenomeTools

Introduction

Typically use in conjunction with bedtools and bedops.

Includes AnnotationSketch, which is able to render a PNG image from a gff file.

Its commands start with a gt and then a subcommand, such as gff3validator or sketch.

Tools

Repfind

the gt suffixerator program has to be run first, to create necessary indeices and other useful files

gt suffixerator -db Repfind-example.fna -indexname repidx2 -v -dna -suf -tis -lcp -ssp -pl

Note how the mnemonics are not great, particularly db meaning input file. Then we can try

gt repfind -f -r -l 4 -ii repidx2

Despite the -r may be meaning reverse, as in reverse strand here, it is not. It actually refers to the same strand, but in the reverse reading direction, which seems futile. For reading the reverse strand, -p is required.

the -outfmt can be interesting, though maybe not useful. See the help for more details ... multple definitions need only be separated by whitespace.

This is a Stefan Kurtz contribution, and can be found in the code under

genometools-1.5.9/src/tools/gt_repfind.c