genometools

Versatile toolkit for analyzing and manipulating genomic sequences and annotations

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Versatile open source genome analysis software

gt

Validate a GFF3 annotation file$ gt gff3 -tidy input.gff3 > output.gff3

Extract sequences from a genome FASTA file using GFF coordinates$ gt extractseq -matchdesc -seqfile genome.fa input.gff3 > sequences.fa

Convert between sequence file formats (GFF to GFF3)$ gt gff3validator input.gff > validated.gff3