GFF Utilities: GffRead and GffCompare

Mihaela Pertea, Geo Pertea

Research output: Contribution to journalArticle

Abstract

Summary: GTF (Gene Transfer Format) and GFF (General Feature Format) are popular file formats used by bioinformatics programs to represent and exchange information about various genomic features, such as gene and transcript locations and structure. GffRead and GffCompare are open source programs that provide extensive and efficient solutions to manipulate files in a GTF or GFF format. While GffRead can convert, sort, filter, transform, or cluster genomic features, GffCompare can be used to compare and merge different gene annotations. Availability and implementation: GFF utilities are implemented in C++ for Linux and OS X and released as open source under an MIT license ( https://github.com/gpertea/gffread, https://github.com/gpertea/gffcompare).

Original languageEnglish (US)
Article number304
JournalF1000Research
Volume9
DOIs
StatePublished - 2020

Keywords

  • GTF and GFF file formats
  • Gene annotation
  • Transcriptome analysis

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Immunology and Microbiology(all)
  • Pharmacology, Toxicology and Pharmaceutics(all)

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