GFF Utilities: GffRead and GffCompare
2020/09/09 by Geo Pertea, Mihaela Pertea · 53 citations
Biochemistry, Genetics and Molecular Biology · #Gene expression and cancer classification #Genomics and Phylogenetic Studies #Machine Learning in Bioinformatics
paper · pdf · doi:10.12688/f1000research.23297.2
openalex publication_date 2020/09/09 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/30
Abstract
<ns4:p><ns4:bold>Summary:</ns4:bold> 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.</ns4:p><ns4:p> <ns4:bold>Availability and implementation:</ns4:bold> GFF utilities are implemented in C++ for Linux and OS X and released as open source under an MIT license (<ns4:ext-link xmlns:ns3="http://www.w3.org/1999/xlink" ext-link-type="uri" ns3:href="https://github.com/gpertea/gffread">https://github.com/gpertea/gffread</ns4:ext-link>, <ns4:ext-link xmlns:ns3="http://www.w3.org/1999/xlink" ext-link-type="uri" ns3:href="https://github.com/gpertea/gffcompare">https://github.com/gpertea/gffcompare</ns4:ext-link>).</ns4:p>
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