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GraphAligner: Rapid and Versatile Sequence-to-Graph Alignment

View ORCID ProfileMikko Rautiainen, Tobias Marschall
doi: https://doi.org/10.1101/810812
Mikko Rautiainen
1Center for Bioinformatics, Saarland University, Saarbrücken, Germany
2Max Planck Institute for Informatics, Saarbrücken, Germany
3Saarbrücken Graduate School for Computer Science, Saarbrücken, Germany
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  • ORCID record for Mikko Rautiainen
Tobias Marschall
1Center for Bioinformatics, Saarland University, Saarbrücken, Germany
2Max Planck Institute for Informatics, Saarbrücken, Germany
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  • For correspondence: t.marschall@mpi-inf.mpg.de
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Abstract

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

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-ND 4.0 International license.
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Posted October 21, 2019.
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GraphAligner: Rapid and Versatile Sequence-to-Graph Alignment
Mikko Rautiainen, Tobias Marschall
bioRxiv 810812; doi: https://doi.org/10.1101/810812
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GraphAligner: Rapid and Versatile Sequence-to-Graph Alignment
Mikko Rautiainen, Tobias Marschall
bioRxiv 810812; doi: https://doi.org/10.1101/810812

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