The GFF3toolkit: QC and Merge Pipeline for Genome Annotation

Mei-Ju May Chen; Han Lin; Li-Mei Chiang; Christopher P Childers; Monica F Poelchau

doi:10.1007/978-1-4939-8775-7_7

The GFF3toolkit: QC and Merge Pipeline for Genome Annotation

Methods Mol Biol. 2019:1858:75-87. doi: 10.1007/978-1-4939-8775-7_7.

Authors

Mei-Ju May Chen¹, Han Lin¹, Li-Mei Chiang¹, Christopher P Childers², Monica F Poelchau³

Affiliations

¹ Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei, Taiwan.
² Agricultural Research Service, National Agricultural Library, USDA, Beltsville, MD, USA. christopher.childers@ars.usda.gov.
³ Agricultural Research Service, National Agricultural Library, USDA, Beltsville, MD, USA. monica.poelchau@ars.usda.gov.

PMID: 30414112
DOI: 10.1007/978-1-4939-8775-7_7

Abstract

The GFF3toolkit ( https://github.com/NAL-i5K/GFF3toolkit ) supported by the i5k Workspace@NAL provides a suite of tools to handle gene annotations in GFF3 format from arthropod genome projects and their research communities. To improve GFF3 formatting of gene annotations, a quality control and merge procedure is proposed along with the GFF3toolkit. In particular, the toolkit provides functions to sort a GFF3 file, detect GFF3 format errors, merge two GFF3 files, and generate biological sequences from a GFF3 file. This chapter explains when and how to use the provided tools to obtain nonredundant arthropod gene sets in high quality.

Keywords: Arthropods; Community annotation; GFF3; Gene annotations; Genomics; I5k; Insects.

Publication types

Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Animals
Computational Biology / methods*
Genome, Insect*
High-Throughput Nucleotide Sequencing / methods
Insecta / genetics*
Molecular Sequence Annotation / methods*
Quality Control*
Sequence Analysis, DNA / methods*
Software*