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SPAligner: Alignment of Long Diverged Molecular Sequences to Assembly Graphs

View ORCID ProfileTatiana Dvorkina, Dmitry Antipov, Anton Korobeynikov, Sergey Nurk
doi: https://doi.org/10.1101/744755
Tatiana Dvorkina
Center for Algorithmic Biotechnology, St. Petersburg State University, St. Petersburg, Russia d.antipov@spbu.ru
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  • ORCID record for Tatiana Dvorkina
  • For correspondence: t.dvorkina@spbu.ru d.antipov@spbu.ru
Dmitry Antipov
Center for Algorithmic Biotechnology, St. Petersburg State University, St. Petersburg, Russia d.antipov@spbu.ru
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  • For correspondence: d.antipov@spbu.ru
Anton Korobeynikov
Center for Algorithmic Biotechnology, Department of Statistical Modelling, St. Petersburg State University, St. Petersburg, Russia a.korobeynikov@spbu.ru
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Sergey Nurk
Genome Informatics Section, National Institutes of Health, Bethesda MD, USA
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Abstract

Background Graph-based representation of genome assemblies has been recently used in different applications — from gene finding to haplotype separation. While most of these applications are based on the alignment of molecular sequences to assembly graphs, existing software tools for finding such alignments have important limitations.

Results We present a novel SPAligner tool for aligning long diverged molecular sequences to assembly graphs and demonstrate that SPAligner is an efficient solution for mapping third generation sequencing data and can also facilitate the identification of known genes in complex metagenomic datasets.

Conclusions Our work will facilitate accelerating the development of graph-based approaches in solving sequence to genome assembly alignment problem. SPAligner is implemented as a part of SPAdes tools library and is available on https://github.com/ablab/spades/archive/spaligner-paper.zip.

Footnotes

  • https://github.com/ablab/spades/releases/tag/spaligner-paper

  • https://figshare.com/s/b0dc3f715e0224e3e962

  • List of abbreviations

    ED
    edit distance
    ARG
    antibiotic resistance gene
    AMR
    antimicrobial resistance
  • 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 August 23, 2019.
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    SPAligner: Alignment of Long Diverged Molecular Sequences to Assembly Graphs
    Tatiana Dvorkina, Dmitry Antipov, Anton Korobeynikov, Sergey Nurk
    bioRxiv 744755; doi: https://doi.org/10.1101/744755
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    SPAligner: Alignment of Long Diverged Molecular Sequences to Assembly Graphs
    Tatiana Dvorkina, Dmitry Antipov, Anton Korobeynikov, Sergey Nurk
    bioRxiv 744755; doi: https://doi.org/10.1101/744755

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