PCI Math Comp Biol

307

Title *

HairSplitter: haplotype assembly from long, noisy readsuse asterix (*) to get italics

Authors *

Roland Faure, Dominique Lavenier, Jean-François FlotPlease use the format "First name initials family name" as in "Marie S. Curie, Niels H. D. Bohr, Albert Einstein, John R. R. Tolkien, Donna T. Strickland"

Year *

2024

Picture *

Abstract *

Long-read assemblers face challenges in discerning closely related viral or bacterial strains, often collapsing similar strains in a single sequence. This limitation has been hampering metagenome analysis, where diverse strains may harbor crucial functional distinctions. We introduce a novel software, HairSplitter, designed to retrieve strains from a strain-oblivious assembly and long reads. The method uses a custom variant calling pro- cess to operate with erroneous long reads and introduces a new read clustering algorithm to recover an a priori unknown number of strains. On noisy long reads, HairSplitter can recover more strains while being faster than state-of-the-art tools, both in the viral and the bacterial case.

Indicate the full web address (DOI or URL) giving public access to these data (if you have any problems with the deposit of your data, please contact contact@mcb.peercommunityin.org). In case all raw data are included in the preprint, indicate the DOI or URL of the preprint. *

https://doi.org/10.5281/zenodo.10495032You should fill this box only if you chose 'All or part of the results presented in this preprint are based on data'. URL must start with http:// or https://

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Indicate the full web address (DOI, SWHID or URL) giving public access to these codes (if you have any problems with the deposit of your codes, please contact contact@mcb.peercommunityin.org). In case all raw codes are included in the preprint, indicate the DOI or URL of the preprint. *

https://github.com/rolandfaure/hairsplitterYou should fill this box only if you chose 'Codes have been used in this study'. URL must start with http:// or https://

Keywords (optional)

Metagenomes; Metaviromes; Haplotyping; Genome assembly; Strain separation

Methods that require specific expertise (optional)

NonePlease indicate the methods that may require specialised expertise during the peer review process (use a comma to separate various required expertises).

Thematic fields *

Design and analysis of algorithms, Development, Genomics and Transcriptomics, Probability and statistics

Suggested reviewers - Suggest up to 10 reviewers (provide names and Email addresses). (Optional)

Paola Bonizzoni bonizzoni@disco.unimib.it, Tobias Marschall tobias.marshall@hhu.de, Nicola Segata nicola.segata@unitn.it, Sergey Koren sergey.koren@nih.gov, Chirag Jain chirag@iisc.ac.in, Jue Ruan jys@agis.org.cn, Sergey Koren [sergey.koren@nih.gov] suggested: I suggest Arang Rhie (Arang.rhie@nih.gov) or Dmitry Antipov (dmitry.antipov@nih.gov) as alternate reviewers. No need for them to be recommenders of PCI Math Comp Biol. Please do not suggest reviewers for whom there might be a conflict of interest. Reviewers are not allowed to review preprints written by close colleagues (with whom they have published in the last four years, with whom they have received joint funding in the last four years, or with whom they are currently writing a manuscript, or submitting a grant proposal), or by family members, friends, or anyone for whom bias might affect the nature of the review - see the code of conduct

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Submission date

2024-02-15 10:17:04

Recommender

Giulio Ermanno Pibiri

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