Nanopore sequencing and assembly of a human genome with ultra-long reads

Sequences of 95 humanMHChaplotypes reveal extreme coding variation in genes other than highly polymorphicHLA class IandII

(2017) Paul J. Norman et al.   GENOME RESEARCH

Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly

(2017) Valerie A. Schneider et al.   GENOME RESEARCH

Canu: scalable and accurate long-read assembly via adaptivek-mer weighting and repeat separation

(2017) Sergey Koren et al.   GENOME RESEARCH

Sequencing and de novo assembly of 150 genomes from Denmark as a population reference

(2017) Lasse Maretty et al.   NATURE

Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genome

(2017) Derek M Bickhart et al.   NATURE GENETICS

Detecting DNA cytosine methylation using nanopore sequencing

(2017) Jared T Simpson et al.   NATURE METHODS

Mapping DNA methylation with high-throughput nanopore sequencing

(2017) Arthur C Rand et al.   NATURE METHODS

de novo assembly and population genomic survey of natural yeast isolates with the Oxford Nanopore MinION sequencer

(2017) Benjamin Istace et al.   GigaScience

Assemblytics: a web analytics tool for the detection of variants from an assembly

(2016) Maria Nattestad et al.   BIOINFORMATICS

Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences

(2016) Heng Li   BIOINFORMATICS

Nanopore sequencing detects structural variants in cancer

(2016) Alexis L. Norris et al.   CANCER BIOLOGY & THERAPY

A reference data set of 5.4 million phased human variants validated by genetic inheritance from sequencing a three-generation 17-member pedigree

(2016) Michael A. Eberle et al.   GENOME RESEARCH

Real-time, portable genome sequencing for Ebola surveillance

(2016) Joshua Quick et al.   NATURE

De novo assembly and phasing of a Korean human genome

(2016) Jeong-Sun Seo et al.   NATURE

Long-read sequence assembly of the gorilla genome

(2016) D. Gordon et al.   SCIENCE

Fast and sensitive mapping of nanopore sequencing reads with GraphMap

(2016) Ivan Sović et al.   Nature Communications

Long-read sequencing and de novo assembly of a Chinese genome

(2016) Lingling Shi et al.   Nature Communications

High-Accuracy HLA Type Inference from Whole-Genome Sequencing Data Using Population Reference Graphs

(2016) Alexander T. Dilthey et al.   PLoS Computational Biology

Extensive sequencing of seven human genomes to characterize benchmark reference materials

(2016) Justin M. Zook et al.   Scientific Data

A global reference for human genetic variation

(2015) Richard A. Gibbs et al.   NATURE

Assembling large genomes with single-molecule sequencing and locality-sensitive hashing

(2015) Konstantin Berlin et al.   NATURE BIOTECHNOLOGY

Improved genome inference in the MHC using a population reference graph

(2015) Alexander Dilthey et al.   NATURE GENETICS

SpeedSeq: ultra-fast personal genome analysis and interpretation

(2015) Colby Chiang et al.   NATURE METHODS

Assembly and diploid architecture of an individual human genome via single-molecule technologies

(2015) Matthew Pendleton et al.   NATURE METHODS

A complete bacterial genome assembled de novo using only nanopore sequencing data

(2015) Nicholas J Loman et al.   NATURE METHODS

Improved data analysis for the MinION nanopore sequencer

(2015) Miten Jain et al.   NATURE METHODS

Genetic variation and the de novo assembly of human genomes

(2015) Mark J. P. Chaisson et al.   NATURE REVIEWS GENETICS

Nanopores Discriminate among Five C5-Cytosine Variants in DNA

(2014) Zachary L. Wescoe et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Integrating human sequence data sets provides a resource of benchmark SNP and indel genotype calls

(2014) Justin M Zook et al.   NATURE BIOTECHNOLOGY

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

(2014) Bruce J. Walker et al.   PLoS One

LUMPY: a probabilistic framework for structural variant discovery

(2014) Ryan M Layer et al.   GENOME BIOLOGY

Detection and mapping of 5-methylcytosine and 5-hydroxymethylcytosine with nanopore MspA

(2013) A. H. Laszlo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory

(2012) Mark J Chaisson et al.   BMC BIOINFORMATICS

Cactus Graphs for Genome Comparisons

(2011) Benedict Paten et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

An integrated semiconductor device enabling non-optical genome sequencing

(2011) Jonathan M. Rothberg et al.   NATURE

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Measurement of telomere length by the Southern blot analysis of terminal restriction fragment lengths

(2010) Masayuki Kimura et al.   Nature Protocols

Single-molecule sequencing of an individual human genome

(2009) Dmitry Pushkarev et al.   NATURE BIOTECHNOLOGY

Using native and syntenically mapped cDNA alignments to improve de novo gene finding

(2008) Mario Stanke et al.   BIOINFORMATICS

Analysis of the largest tandemly repeated DNA families in the human genome

(2008) Peter E Warburton et al.   BMC GENOMICS

The complete genome of an individual by massively parallel DNA sequencing

(2008) David A. Wheeler et al.   NATURE

Accurate whole human genome sequencing using reversible terminator chemistry

(2008) David R. Bentley et al.   NATURE