RT Journal Article
SR Electronic
T1 GraphAligner: Rapid and Versatile Sequence-to-Graph Alignment
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 810812
DO 10.1101/810812
A1 Mikko Rautiainen
A1 Tobias Marschall
YR 2019
UL http://biorxiv.org/content/early/2019/10/21/810812.abstract
AB Genome graphs can represent genetic variation and sequence uncertainty. Aligning sequences to genome graphs is key to many applications, including error correction, genome assembly, and genotyping of variants in a pan-genome graph. Yet, so far this step is often prohibitively slow. We present GraphAligner, a tool for aligning long reads to genome graphs. Compared to state-of-the-art tools, GraphAligner is 12x faster and uses 5x less memory, making it as efficient as aligning reads to linear reference genomes. When employing GraphAligner for error correction, we find it to be almost 3x more accurate and over 15x faster than extant tools.Availability Package manager https://anaconda.org/bioconda/graphaligner and source code: https://github.com/maickrau/GraphAligner