LiftoffTools: a toolkit for comparing gene annotations mapped between genome assemblies [version 1; peer review: 1 approved with reservations]

In 2020 we published Liftoff, which was the first standalone tool specifically designed for transferring gene annotations between genome assemblies of the same or closely related species. While the gene content is expected to be very similar in closely related genomes, the differences may be biologi...

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Bibliographic Details
Published inF1000 research Vol. 11; p. 1230
Main Authors Shumate, Alaina, Salzberg, Steven
Format Journal Article
LanguageEnglish
Published 2022
Subjects
Genome annotation
Bioinformatics
Genomics
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Summary:In 2020 we published Liftoff, which was the first standalone tool specifically designed for transferring gene annotations between genome assemblies of the same or closely related species. While the gene content is expected to be very similar in closely related genomes, the differences may be biologically consequential, and a computational method to extract all gene-related differences should prove useful in the analysis of such genomes. Here we present LiftoffTools, a toolkit to automate the detection and analysis of gene sequence variants, synteny, and gene copy number changes.  We provide a description of the toolkit and an example of its use comparing genes mapped between two human genome assemblies.
ISSN:2046-1402
2046-1402
DOI:10.12688/f1000research.124059.1