Abstract
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).
Highlights
Many biomedical research applications employ pipelines to systematically analyze the gene content in a genome
Due to the explosion in transcriptomic data available, these pipelines routinely involve processing enormous amounts of data, and require efficient bioinformatics tools that can handle multiple annotation and sequence files in order to speed up the genomic analysis
Such tools usually exchange and employ information about genes, transcripts or other genomic features in a tab-delimited text file format commonly known as GFF (General Feature Format)
Summary
Many biomedical research applications employ pipelines to systematically analyze the gene content in a genome. Due to the explosion in transcriptomic data available, these pipelines routinely involve processing enormous amounts of data, and require efficient bioinformatics tools that can handle multiple annotation and sequence files in order to speed up the genomic analysis Such tools usually exchange and employ information about genes, transcripts or other genomic features in a tab-delimited text file format commonly known as GFF (General Feature Format). In this paper we provide detailed descriptions of the specific functions provided by our GFF utilities
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