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...
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| Format: | Online |
| Language: | English |
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2015
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| Online Access: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4877053/ |
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pubmed-48770532016-05-23 De novo sequencing and variant calling with nanopores using PoreSeq Szalay, Tamas Golovchenko, Jene A. 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 |
| repository_type |
Open Access Journal |
| institution_category |
Foreign Institution |
| institution |
US National Center for Biotechnology Information |
| building |
NCBI PubMed |
| collection |
Online Access |
| language |
English |
| format |
Online |
| author |
Szalay, Tamas Golovchenko, Jene A. |
| spellingShingle |
Szalay, Tamas Golovchenko, Jene A. De novo sequencing and variant calling with nanopores using PoreSeq |
| author_facet |
Szalay, Tamas Golovchenko, Jene A. |
| author_sort |
Szalay, Tamas |
| title |
De novo sequencing and variant calling with nanopores using PoreSeq |
| title_short |
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_sort |
de novo sequencing and variant calling with nanopores using poreseq |
| 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. |
| publishDate |
2015 |
| url |
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4877053/ |
| _version_ |
1613582914153349120 |