Efficient and unique cobarcoding of second-generation sequencing reads from long DNA molecules enabling cost-effective and accurate sequencing, haplotyping, and de novo assembly

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

(2018) Miten Jain et al.   NATURE BIOTECHNOLOGY

3′ Branch ligation: a novel method to ligate non-complementary DNA to recessed or internal 3′OH ends in DNA or RNA

(2018) Lin Wang et al.   DNA RESEARCH

Identification of balanced chromosomal rearrangements previously unknown among participants in the 1000 Genomes Project: implications for interpretation of structural variation in genomes and the future of clinical cytogenetics

(2017) Zirui Dong et al.   GENETICS IN MEDICINE

Haplotype phasing of whole human genomes using bead-based barcode partitioning in a single tube

(2017) Fan Zhang et al.   NATURE BIOTECHNOLOGY

The sponge microbiome project

(2017) Lucas Moitinho-Silva et al.   GigaScience

Low-pass whole-genome sequencing in clinical cytogenetics: a validated approach

(2016) Zirui Dong et al.   GENETICS IN MEDICINE

HapCUT2: robust and accurate haplotype assembly for diverse sequencing technologies

(2016) Peter Edge et al.   GENOME RESEARCH

Haplotyping germline and cancer genomes with high-throughput linked-read sequencing

(2016) Grace X Y Zheng et al.   NATURE BIOTECHNOLOGY

cPAS-based sequencing on the BGISEQ-500 to explore small non-coding RNAs

(2016) Tobias Fehlmann et al.   Clinical Epigenetics

The whole genome sequences and experimentally phased haplotypes of over 100 personal genomes

(2016) Qing Mao et al.   GigaScience

Co-barcoded sequence reads from long DNA fragments: a cost-effective solution for “perfect genome” sequencing

(2015) Brock A. Peters et al.   Frontiers in Genetics

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

(2014) Justin M Zook et al.   NATURE BIOTECHNOLOGY

Whole-genome haplotyping using long reads and statistical methods

(2014) Volodymyr Kuleshov et al.   NATURE BIOTECHNOLOGY

Haplotype-resolved whole-genome sequencing by contiguity-preserving transposition and combinatorial indexing

(2014) Sasan Amini et al.   NATURE GENETICS

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

Whole-genome haplotype reconstruction using proximity-ligation and shotgun sequencing

(2013) Siddarth Selvaraj et al.   NATURE BIOTECHNOLOGY

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

(2013) Jason D Buenrostro et al.   NATURE METHODS

Accurate whole-genome sequencing and haplotyping from 10 to 20 human cells

(2012) Brock A. Peters et al.   NATURE

A comprehensively molecular haplotype-resolved genome of a European individual

(2011) E.-K. Suk et al.   GENOME RESEARCH

Fosmid-based whole genome haplotyping of a HapMap trio child: evaluation of Single Individual Haplotyping techniques

(2011) Jorge Duitama et al.   NUCLEIC ACIDS RESEARCH

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Whole-genome molecular haplotyping of single cells

(2010) H Christina Fan et al.   NATURE BIOTECHNOLOGY

Haplotype-resolved genome sequencing of a Gujarati Indian individual

(2010) Jacob O Kitzman et al.   NATURE BIOTECHNOLOGY

Direct determination of molecular haplotypes by chromosome microdissection

(2010) Li Ma et al.   NATURE METHODS

Replication of individual DNA molecules under electronic control using a protein nanopore

(2010) Felix Olasagasti et al.   Nature Nanotechnology

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Elongation and migration of single DNA molecules in microchannels using oscillatory shear flows

(2009) Kyubong Jo et al.   LAB ON A CHIP

Human Genome Sequencing Using Unchained Base Reads on Self-Assembling DNA Nanoarrays

(2009) R. Drmanac et al.   SCIENCE