npm

gffread

Convert and filter GFF/GTF files, extract FASTA sequences

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About

GFF/GTF format conversions, region filtering, FASTA sequence extraction

Commands

gffread

Examples

Convert GFF3 to GTF format$ gffread input.gff3 -T -o output.gtf
Extract FASTA sequences for genomic regions in GFF file$ gffread input.gff3 -g genome.fasta -w output.fasta
Filter GFF file to extract features in specific region$ gffread input.gff3 -R -r chr1:1000-2000 -o filtered.gff3