Sunday Morning Insight: "No Need for the Map of a Cat, Mr Feynman" or The Long Game in Nanopore Sequencing.

About 5 weeks ago, we wondered how we could tell if the world was changing right before our eyes ?  well, this is happening, instance #2 just got more real:

Nanopore sequencing and assembly of a human genome with ultra-long reads by Miten Jain, Sergey Koren, Josh Quick, Arthur C Rand, Thomas A Sasani, John R Tyson, Andrew D Beggs, Alexander T Dilthey, Ian T Fiddes, Sunir Malla, Hannah Marriott, Karen H Miga, Tom Nieto, Justin O'Grady, Hugh E Olsen, Brent S Pedersen, Arang Rhie, Hollian Richardson, Aaron Quinlan, Terrance P Snutch, Louise Tee, Benedict Paten, Adam M. Phillippy, Jared T Simpson, Nicholas James Loman, Matthew Loose

Nanopore sequencing is a promising technique for genome sequencing due to its portability, ability to sequence long reads from single molecules, and to simultaneously assay DNA methylation. However until recently nanopore sequencing has been mainly applied to small genomes, due to the limited output attainable. We present nanopore sequencing and assembly of the GM12878 Utah/Ceph human reference genome generated using the Oxford Nanopore MinION and R9.4 version chemistry. We generated 91.2 Gb of sequence data (~30x theoretical coverage) from 39 flowcells. De novo assembly yielded a highly complete and contiguous assembly (NG50 ~3Mb). We observed considerable variability in homopolymeric tract resolution between different basecallers. The data permitted sensitive detection of both large structural variants and epigenetic modifications. Further we developed a new approach exploiting the long-read capability of this system and found that adding an additional 5x-coverage of "ultra-long" reads (read N50 of 99.7kb) more than doubled the assembly contiguity. Modelling the repeat structure of the human genome predicts extraordinarily contiguous assemblies may be possible using nanopore reads alone. Portable de novo sequencing of human genomes may be important for rapid point-of-care diagnosis of rare genetic diseases and cancer, and monitoring of cancer progression. The complete dataset including raw signal is available as an Amazon Web Services Open Dataset at: https://github.com/nanopore-wgs-consortium/NA12878.

Here is some context:

• Oxford Nanopore Finally Giving Hope To Biologist’s Dreams

And previously on Nuit Blanche:

• Sunday Morning Insight: Escaping Feynman's NP-Hard "Map of a Cat": Genomic Sequencing Edition
• Sunday Morning Insight: What Happens When You Cross into P Territory ?
• Sunday Morning Insight: And You, What Are You Waiting For ? 
• Sunday Morning Insight: The Second Inflection Point in Genome Sequencing 
• Predicting the Future: The Steamrollers and Machine Learning.  
• Predicting the Future: The Steamrollers

  Credit: NASA, JPL



Join the CompressiveSensing subreddit or the Google+ Community or the Facebook page and post there !
Liked this entry ? subscribe to Nuit Blanche's feed, there's more where that came from. You can also subscribe to Nuit Blanche by Email, explore the Big Picture in Compressive Sensing or the Matrix Factorization Jungle and join the conversations on compressive sensing, advanced matrix factorization and calibration issues on Linkedin.