Ultralow-input single-tube linked-read library method enables short-read second-generation sequencing systems to routinely generate highly accurate and economical long-range sequencing information

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

(2019) Ou Wang et al.   GENOME RESEARCH

An open resource for accurately benchmarking small variant and reference calls

(2019) Justin M. Zook et al.   NATURE BIOTECHNOLOGY

Assembly of long, error-prone reads using repeat graphs

(2019) Mikhail Kolmogorov et al.   NATURE BIOTECHNOLOGY

cloudSPAdes: assembly of synthetic long reads using de Bruijn graphs

(2019) Ivan Tolstoganov et al.   BIOINFORMATICS

Targeted short read sequencing and assembly of re-arrangements and candidate gene loci provide megabase diplotypes

(2019) GiWon Shin et al.   NUCLEIC ACIDS RESEARCH

Multi-platform discovery of haplotype-resolved structural variation in human genomes

(2019) Mark J. P. Chaisson et al.   Nature Communications

Longshot enables accurate variant calling in diploid genomes from single-molecule long read sequencing

(2019) Peter Edge et al.   Nature Communications

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

(2018) Miten Jain et al.   NATURE BIOTECHNOLOGY

High-quality genome sequences of uncultured microbes by assembly of read clouds

(2018) Alex Bishara et al.   NATURE BIOTECHNOLOGY

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

(2017) Fan Zhang et al.   NATURE BIOTECHNOLOGY

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

TruSPAdes: barcode assembly of TruSeq synthetic long reads

(2016) Anton Bankevich et al.   NATURE METHODS

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

(2015) Felipe A. Simão et al.   BIOINFORMATICS

An integrated map of structural variation in 2,504 human genomes

(2015) Peter H. Sudmant et al.   NATURE

A global reference for human genetic variation

(2015) Richard A. Gibbs et al.   NATURE

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

(2015) Nicholas J Loman et al.   NATURE METHODS

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

(2014) Sasan Amini et al.   NATURE GENETICS

Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions

(2013) Joshua N Burton et al.   NATURE BIOTECHNOLOGY

The genome sequence of the colonial chordate, Botryllus schlosseri

(2013) Ayelet Voskoboynik et al.   eLife

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

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

(2012) Brock A. Peters et al.   NATURE

An integrated semiconductor device enabling non-optical genome sequencing

(2011) Jonathan M. Rothberg et al.   NATURE

Rapid, low-input, low-bias construction of shotgun fragment libraries by high-density in vitro transposition

(2010) Andrew Adey et al.   GENOME BIOLOGY

The HLA genomic loci map: expression, interaction, diversity and disease

(2009) Takashi Shiina et al.   JOURNAL OF HUMAN GENETICS

A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning

(2008) A. Valouev et al.   GENOME RESEARCH

The Complete Genome Sequence of Escherichia coli DH10B: Insights into the Biology of a Laboratory Workhorse

(2008) T. Durfee et al.   JOURNAL OF BACTERIOLOGY

Accurate whole human genome sequencing using reversible terminator chemistry

(2008) David R. Bentley et al.   NATURE

Real-Time DNA Sequencing from Single Polymerase Molecules

(2008) J. Eid et al.   SCIENCE