A new nanopore sequencing kit is now being tested by\u202fa number of\u202fdevelopers in the nanopore user community.\u202f\u202fThe kit features a modified enzyme, tweaked run conditions and a further improved\u202fbasecalling\u202fmodel in the\u202fBonito basecaller. These improvements have produced raw single-molecule, single-pass sequencing reads above a modal 99% accuracy, or Q20+\u202fin external\u202fusers\u2019\u202fhands, as well as internally.\u202f\u202f The improved software also allows optional filtering of lower-quality reads, moving the mean accuracy closer to Q20 without sacrificing read length.<\/p>\n
This novel chemistry, as first mentioned at the Nanopore Community Meeting in December, makes use of\u202fOxford Nanopore\u2019s existing electronic nanopore sensing platform\u202fto deliver improved accuracy on an individual read\u202f(\u201craw read\u201d)\u202fbasis.<\/p>\n
Oxford Nanopore recently released\u202fBonito v0.3.6 \u2014 an updated\u202fbasecaller\u202fthat has been shown to\u202fboost performance to\u202fa modal\u202fraw accuracy of\u202f98.3% with existing\u202fin-field sequencing chemistry. This\u202fbasecaller\u202fupdate can also be\u202fused to re-analyse older data\u202fand significantly improve it.<\/p>\n
Oxford Nanopore\u2019s R&D teams are currently working on additional methods to\u202fdrive further improvement of\u202fsingle-molecule\u202fbasecalling\u202fover the course of 2021.\u202f\u202f\u202fThis includes a potential\u202fmulti-pass chemistry\u202fdesigned to yield\u202fhighly accurate single-molecule consensus reads,\u202fwithout sacrificing read length. Work has also advanced on native calling of natural base modifications at the single molecule level.\u202f Further updates\u202fon this pipeline will be provided in due course.<\/p>\n
New chemistry<\/strong><\/p>\n An early version of the\u202f\u201cQ20+\u201d\u202fkit is now in use by initial developer sites around the world, who are currently providing feedback that will inform further development of the final kit and\u202fbasecalling\u202falgorithms.\u202f Oxford Nanopore intends to broaden the early access phase in due course and will provide updates in the coming weeks.<\/p>\n \u201cIt\u2019s great to see that we can replicate the performance seen by Oxford Nanopore of the new Q20+ chemistry,\u201d\u202fsaid Professor Matt Loose, from\u202fDeepSeq\u202fat the University of Nottingham.\u202f\u201cThe yield is good and\u202fpore\u202foccupancy is fantastic. We’re looking forward to trying this chemistry on other samples to better measure the improvements to assembly and consensus accuracy for our more challenging projects very soon.\u201d<\/p>\n \u201cI find it pretty amazing that even this early access version of the kit can produce\u202fgood throughput\u202fhighly accurate single pass data within ~1day of sequencing a complex metagenome sample.\u201d\u202fsaid Rasmus Kirkegaard, University of Vienna, \u201cI am sure\u202fraw read\u202fQ20 any length sequencing will be a game changer!\u201d.<\/p>\n Nanopore sequencing uniquely combines\u202fa number of\u202fproperties, including sequencing\u202fDNA or RNA fragments\u202fof any length, real-time data generation and retention of base modifications, which alongside very high single molecule accuracy gives rich data about the underlying biology in a sample.<\/p>\n Very high single molecule accuracy supports the generation of high-quality consensus sequences, where the molecule is read multiple times, allowing for the generation of\u202freference-quality genomes.<\/p>\n Oxford Nanopore has driven continuous improvement in accuracy of\u202fits sequencing platform since launch, through combining new sequencing chemistries with continuously evolving data analysis algorithms.\u202f In addition to high single-pass accuracy, the nanopore platform is now able to deliver\u202fsingle molecule consensus accuracy of 99.995% with UMIs,\u202fand\u202fQ50\u202f(99.999%)\u202fconsensus sequencing data. Nanopore sequencing outperforms traditional short read technologies on its ability to elucidate\u202fstructural\u202fvariants, and\u202fcan provide SNV calling accuracy of\u202f99.92 (F1) on the current R9.4 flow\u202fcells.\u202fFor further information on the tool sets that support these performances please visit\u202fthe nanopore sequencing accuracy page<\/p>\n Higher\u202fPromethION\u202fyields drive cost efficiencies for high throughput sequencing<\/strong><\/p>\n In addition to developments on\u202faccuracy, Oxford Nanopore\u202fannounced at NCM\u202fin December 2020,\u202fthe release of upgraded\u202fPromethION\u202fflow cells, that are driving consistently higher yields in\u202fusers\u202fhands.\u202f\u202fThis has supported a\u202frecent in-field record of 245Gb from a single\u202fPromethION\u202fflow cell,\u202for the equivalent of nearly three 30X human genomes on a single flow cell.\u202f Noting that a\u202fPromethION\u202fcan run up to 48 flow cells,\u202fand that\u202fPromethION\u202fflow cells can be purchased for as little as $625, this development\u202fsupports ultra-high throughput nanopore sequencing.\u202f\u202fTo find out more about\u202fPromethION, visit the website.<\/p>\n","protected":false},"excerpt":{"rendered":" A new nanopore sequencing kit is now being tested by\u202fa number of\u202fdevelopers in the nanopore user community.\u202f\u202fThe kit features a modified enzyme, tweaked run conditions and a further improved\u202fbasecalling\u202fmodel in the\u202fBonito basecaller. These improvements have produced raw single-molecule, single-pass sequencing reads above a modal 99% accuracy, or Q20+\u202fin external\u202fusers\u2019\u202fhands, as well as internally.\u202f\u202f The improved […]<\/p>\n","protected":false},"author":2,"featured_media":3678,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":[],"categories":[1],"tags":[],"jetpack_featured_media_url":"https:\/\/oxgenimport.ge\/wp-content\/uploads\/2022\/11\/blog-single-img-1.jpg","_links":{"self":[{"href":"https:\/\/oxgenimport.ge\/index.php\/wp-json\/wp\/v2\/posts\/3992"}],"collection":[{"href":"https:\/\/oxgenimport.ge\/index.php\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/oxgenimport.ge\/index.php\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/oxgenimport.ge\/index.php\/wp-json\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/oxgenimport.ge\/index.php\/wp-json\/wp\/v2\/comments?post=3992"}],"version-history":[{"count":20,"href":"https:\/\/oxgenimport.ge\/index.php\/wp-json\/wp\/v2\/posts\/3992\/revisions"}],"predecessor-version":[{"id":10200,"href":"https:\/\/oxgenimport.ge\/index.php\/wp-json\/wp\/v2\/posts\/3992\/revisions\/10200"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/oxgenimport.ge\/index.php\/wp-json\/wp\/v2\/media\/3678"}],"wp:attachment":[{"href":"https:\/\/oxgenimport.ge\/index.php\/wp-json\/wp\/v2\/media?parent=3992"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/oxgenimport.ge\/index.php\/wp-json\/wp\/v2\/categories?post=3992"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/oxgenimport.ge\/index.php\/wp-json\/wp\/v2\/tags?post=3992"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}