Targeted nanopore sequencing by real-time mapping of raw electrical signal with UNCALLED
- 29 November 2020
- journal article
- research article
- Published by Springer Science and Business Media LLC in Nature Biotechnology
- Vol. 39 (4), 431-+
- https://doi.org/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 (), 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 29.6x coverage using one MinION flowcell, enabling accurate detection of single-nucleotide polymorphisms, insertions and deletions, structural variants and methylation in these genes.Funding Information
- U.S. Department of Health & Human Services | NIH | National Human Genome Research Institute (1R01HG009190)
- National Science Foundation (DBI-1350041)
This publication has 49 references indexed in Scilit:
- Alu elements: know the SINEsGenome Biology, 2011
- A fast, lock-free approach for efficient parallel counting of occurrences of k-mersBioinformatics, 2011
- COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in CancerNucleic Acids Research, 2010
- BEDTools: a flexible suite of utilities for comparing genomic featuresBioinformatics, 2010
- Fast and accurate long-read alignment with Burrows–Wheeler transformBioinformatics, 2010
- Ultrafast and memory-efficient alignment of short DNA sequences to the human genomeGenome Biology, 2009
- X-inactivation profile reveals extensive variability in X-linked gene expression in femalesNature, 2005
- Exposing the MYtH about base excision repair and human inherited diseaseHuman Molecular Genetics, 2003
- The UCSC Genome Browser DatabaseNucleic Acids Research, 2003
- Note on a Method for Calculating Corrected Sums of Squares and ProductsTechnometrics, 1962