What question did this study set out to answer?

Provide efficient, open-source software utilities to manipulate, filter, convert, and compare genomic annotation files in standard GTF and GFF formats.

April 28, 2020F1000ResearchOpen Access

GFF Utilities: GffRead and GffCompare

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Provide efficient, open-source software utilities to manipulate, filter, convert, and compare genomic annotation files in standard GTF and GFF formats.
Implemented the utilities GffRead and GffCompare in C++ under an MIT open-source license for Linux and OS X operating systems.
Engineered GffRead to convert, sort, filter, transform, and cluster transcript coordinates and genomic features.
Engineered GffCompare to evaluate, classify, and merge independent transcript assemblies against reference gene annotations.
GffRead enables modular and rapid validation, transformation, and extraction of genomic features across diverse GTF and GFF specifications.
GffCompare accurately characterizes novel versus known transcripts and unifies divergent gene annotation sets across bioinformatics workflows.

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Implication

Software report demonstrates efficient processing and comparison of GTF and GFF genomic annotations, suggesting improved data integration for transcriptomic pipelines.

Cite This Study

Pertea et al. (2020) studied this question.

synapsesocial.com/papers/69d6b4cefca0359822aa819e https://doi.org/10.12688/f1000research.23297.1

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Implication

Software report demonstrates efficient processing and comparison of GTF and GFF genomic annotations, suggesting improved data integration for transcriptomic pipelines.

GFF Utilities: GffRead and GffCompare

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Discussion

Implication

Cite This Study

GFF Utilities: GffRead and GffCompare

Key Points

Discussion

Implication

Cite This Study

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