Targeted nanopore sequencing by real-time mapping of raw electrical signal with UNCALLED.

Kovaka, Sam, Fan, Yunfan, Ni, Bohan, Timp, Winston, Schatz, Michael C (April 2021) Targeted nanopore sequencing by real-time mapping of raw electrical signal with UNCALLED. Nature Biotechnology, 39 (4). pp. 431-441. ISSN 1087-0156

URL: https://www.ncbi.nlm.nih.gov/pubmed/33257863
DOI: 10.1038/s41587-020-0731-9

Abstract

Conventional targeted sequencing methods eliminate many of the benefits of nanopore sequencing, such as the ability to accurately detect structural variants or epigenetic modifications. The ReadUntil method allows nanopore devices to selectively eject reads from pores in real time, which could enable purely computational targeted sequencing. However, this requires rapid identification of on-target reads while most mapping methods require computationally intensive basecalling. We present UNCALLED ( https://github.com/skovaka/UNCALLED ), an open source mapper that rapidly matches streaming of nanopore current signals to a reference sequence. UNCALLED probabilistically considers k-mers that could be represented by the signal and then prunes the candidates based on the reference encoded within a Ferragina-Manzini index. We used UNCALLED to deplete sequencing of known bacterial genomes within a metagenomics community, enriching the remaining species 4.46-fold. UNCALLED also enriched 148 human genes associated with hereditary cancers to 29.6× coverage using one MinION flowcell, enabling accurate detection of single-nucleotide polymorphisms, insertions and deletions, structural variants and methylation in these genes.

Item Type: Paper
Subjects: organism description > bacteria
bioinformatics > computational biology
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > mutations
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > single nucleotide polymorphism
CSHL Authors:
Communities: CSHL labs > Schatz lab
SWORD Depositor: CSHL Elements
Depositing User: CSHL Elements
Date: April 2021
Date Deposited: 07 May 2021 17:28
Last Modified: 07 May 2021 17:28
URI: https://repository.cshl.edu/id/eprint/40051

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