Liftoff: accurate mapping of gene annotations

By Alaina Shumate, Steven L. Salzberg. Bioinform., 2020

749 citations recorded by the source corpus.

MOTIVATION Improvements in DNA sequencing technology and computational methods have led to a substantial increase in the creation of high-quality genome assemblies of many species. To understand the biology of these genomes, annotation of gene features and other functional elements is essential; however for most species, only the reference genome is well-annotated. RESULTS One strategy to annotate new or improved genome assemblies is to map or 'lift over' the genes from a previously-annotated reference genome. Here we describe Liftoff, a new genome annotation lift-over tool capable of mapping genes between two assemblies of the same or closely-related species. Liftoff aligns genes from a reference genome to a target genome and finds the mapping that maximizes sequence identity while preserving the structure of each exon, transcript, and gene. We show that Liftoff can accurately map 99.9% of genes between two versions of the human reference genome with an average sequence identity >99.9%. We also show that Liftoff can map genes across species by successfully lifting over 98.3% of human protein-coding genes to a chimpanzee genome assembly with 98.2% sequence identity. AVAILABILITY AND IMPLEMENTATION Liftoff can be installed via bioconda and PyPI. Additionally, the source code for Liftoff is available at https://github.com/agshumate/Liftoff. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.

Subfields: Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/6a11f5d9e284979e77b82abc60d462183be81a02

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Citations in the corpus

Automated assembly scaffolding using RagTag elevates a new tomato system for high-throughput genome editing (2022, neutral): “5.1, -copies) [1, 3, 49].”
NextDenovo: an efficient error correction and accurate assembly tool for noisy long reads (2024, neutral): “6.3) [44] with the following settings: liftoff -flank 0.1 -sc 0.85 -copies.”
The complete sequence of a human genome (2021, methodology): “To provide an initial annotation, we used both the Comparative Annotation Toolkit (CAT) (39) and Liftoff (40) to project the GENCODE v35 (41) reference annotation onto the T2T-CHM13 assembly.”