GFF Utilities: GffRead and GffCompare

By Geo Pertea, Mihaela Pertea. F1000Research, 2020

1,483 citations recorded by the source corpus.

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).

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/7f16fc679c2c66bbe9d04beaa8af14be834ad178

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In Molecular Biology

1. Alaina Shumate
2. Brandon Wong
3. Mihaela Pertea
4. Geo Pertea

Citations in the corpus

• Automated assembly scaffolding using RagTag elevates a new tomato system for high-throughput genome editing (2022, neutral): “12.3, -y -w -x) [50].”
• Improved transcriptome assembly using a hybrid of long and short reads with StringTie (2021, methodology): “…and full-length isoform analysis Annotated transcript sequences for each species were extracted from the reference genome using gffread [19] with the following command: gffread -w transcripts.fa -g -g reference_genome.fa reference_annotation.gtf We then aligned each long-read dataset…”