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De novo sequencing and variant calling with nanopores using PoreSeq
The single-molecule accuracy of nanopore sequencing has been an area of rapid academic and commercial advancement, but remains challenging for the de novo analysis of genomes. We introduce here a novel algorithm for the error correction of nanopore data, utilizing statistical models of the physical...
Autores principales: | , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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2015
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4877053/ https://www.ncbi.nlm.nih.gov/pubmed/26352647 http://dx.doi.org/10.1038/nbt.3360 |
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author | Szalay, Tamas Golovchenko, Jene A. |
author_facet | Szalay, Tamas Golovchenko, Jene A. |
author_sort | Szalay, Tamas |
collection | PubMed |
description | The single-molecule accuracy of nanopore sequencing has been an area of rapid academic and commercial advancement, but remains challenging for the de novo analysis of genomes. We introduce here a novel algorithm for the error correction of nanopore data, utilizing statistical models of the physical system in order to obtain high accuracy de novo sequences at a range of coverage depths. We demonstrate the technique by sequencing M13 bacteriophage DNA to 99% accuracy at moderate coverage as well as its use in an assembly pipeline by sequencing E. coli and λ DNA at a range of coverages. We also show the algorithm’s ability to accurately classify sequence variants at far lower coverage than existing methods. |
format | Online Article Text |
id | pubmed-4877053 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2015 |
record_format | MEDLINE/PubMed |
spelling | pubmed-48770532016-05-23 De novo sequencing and variant calling with nanopores using PoreSeq Szalay, Tamas Golovchenko, Jene A. Nat Biotechnol Article The single-molecule accuracy of nanopore sequencing has been an area of rapid academic and commercial advancement, but remains challenging for the de novo analysis of genomes. We introduce here a novel algorithm for the error correction of nanopore data, utilizing statistical models of the physical system in order to obtain high accuracy de novo sequences at a range of coverage depths. We demonstrate the technique by sequencing M13 bacteriophage DNA to 99% accuracy at moderate coverage as well as its use in an assembly pipeline by sequencing E. coli and λ DNA at a range of coverages. We also show the algorithm’s ability to accurately classify sequence variants at far lower coverage than existing methods. 2015-09-09 2015-10 /pmc/articles/PMC4877053/ /pubmed/26352647 http://dx.doi.org/10.1038/nbt.3360 Text en http://www.nature.com/authors/editorial_policies/license.html#terms Users may view, print, copy, and download text and data-mine the content in such documents, for the purposes of academic research, subject always to the full Conditions of use:http://www.nature.com/authors/editorial_policies/license.html#terms |
spellingShingle | Article Szalay, Tamas Golovchenko, Jene A. De novo sequencing and variant calling with nanopores using PoreSeq |
title | De novo sequencing and variant calling with nanopores using PoreSeq |
title_full | De novo sequencing and variant calling with nanopores using PoreSeq |
title_fullStr | De novo sequencing and variant calling with nanopores using PoreSeq |
title_full_unstemmed | De novo sequencing and variant calling with nanopores using PoreSeq |
title_short | De novo sequencing and variant calling with nanopores using PoreSeq |
title_sort | de novo sequencing and variant calling with nanopores using poreseq |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4877053/ https://www.ncbi.nlm.nih.gov/pubmed/26352647 http://dx.doi.org/10.1038/nbt.3360 |
work_keys_str_mv | AT szalaytamas denovosequencingandvariantcallingwithnanoporesusingporeseq AT golovchenkojenea denovosequencingandvariantcallingwithnanoporesusingporeseq |