Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes

Characterizing the Major Structural Variant Alleles of the Human Genome

(2019) Peter A. Audano et al.   CELL

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

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

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

Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome

(2019) Aaron M. Wenger et al.   NATURE BIOTECHNOLOGY

Improved assembly and variant detection of a haploid human genome using single‐molecule, high‐fidelity long reads

(2019) Mitchell R. Vollger et al.   ANNALS OF HUMAN GENETICS

A graph-based approach to diploid genome assembly

(2018) Shilpa Garg et al.   BIOINFORMATICS

Versatile genome assembly evaluation with QUAST-LG

(2018) Alla Mikheenko et al.   BIOINFORMATICS

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

Human-Specific NOTCH2NL Genes Affect Notch Signaling and Cortical Neurogenesis

(2018) Ian T. Fiddes et al.   CELL

Comparative Annotation Toolkit (CAT)—simultaneous clade and personal genome annotation

(2018) Ian T. Fiddes et al.   GENOME RESEARCH

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

(2018) Miten Jain et al.   NATURE BIOTECHNOLOGY

Linear assembly of a human centromere on the Y chromosome

(2018) Miten Jain et al.   NATURE BIOTECHNOLOGY

Accurate detection of complex structural variations using single-molecule sequencing

(2018) Fritz J. Sedlazeck et al.   NATURE METHODS

High-resolution comparative analysis of great ape genomes

(2018) Zev N. Kronenberg et al.   SCIENCE

A universal SNP and small-indel variant caller using deep neural networks

(2018) Ryan Poplin et al.   NATURE BIOTECHNOLOGY

Hybrid assembly of ultra-long nanopore reads augmented with 10×-genomics contigs: Demonstrated with a human genome

(2018) Zhanshan (Sam) Ma et al.   GENOMICS

De novo assembly of haplotype-resolved genomes with trio binning

(2018) Sergey Koren et al.   NATURE BIOTECHNOLOGY

Direct determination of diploid genome sequences

(2017) Neil I. Weisenfeld et al.   GENOME RESEARCH

Fast and accurate de novo genome assembly from long uncorrected reads

(2017) Robert Vaser 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

Single molecule real-time DNA sequencing of HLA genes at ultra-high resolution from 126 International HLA and Immunogenetics Workshop cell lines

(2017) T. R. Turner et al.   HLA

Chromosome-scale shotgun assembly using an in vitro method for long-range linkage

(2016) Nicholas H. Putnam et al.   GENOME RESEARCH

Discovery and genotyping of structural variation from long-read haploid genome sequence data

(2016) John Huddleston et al.   GENOME RESEARCH

Phased diploid genome assembly with single-molecule real-time sequencing

(2016) Chen-Shan Chin et al.   NATURE METHODS

Extensive sequencing of seven human genomes to characterize benchmark reference materials

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

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

WhatsHap: Weighted Haplotype Assembly for Future-Generation Sequencing Reads

(2015) Murray Patterson et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

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

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

Global diversity, population stratification, and selection of human copy-number variation

(2015) Peter H. Sudmant et al.   SCIENCE

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

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

Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data

(2013) Chen-Shan Chin et al.   NATURE METHODS

Strand-seq: A unifying tool for studies of chromosome segregation

(2013) Ester Falconer et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species

(2013) Keith R Bradnam et al.   GigaScience

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

Hi–C: A comprehensive technique to capture the conformation of genomes

(2012) Jon-Matthew Belton et al.   METHODS

An integrated map of genetic variation from 1,092 human genomes

(2012)   NATURE

Cactus: Algorithms for genome multiple sequence alignment

(2011) B. Paten et al.   GENOME RESEARCH

Genome structural variation discovery and genotyping

(2011) Can Alkan et al.   NATURE REVIEWS GENETICS

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

(2010) A. McKenna et al.   GENOME RESEARCH

Sequence progressive alignment, a framework for practical large-scale probabilistic consistency alignment

(2008) Benedict Paten et al.   BIOINFORMATICS

Aggressive assembly of pyrosequencing reads with mates

(2008) Jason R. Miller et al.   BIOINFORMATICS

Real-Time DNA Sequencing from Single Polymerase Molecules

(2008) J. Eid et al.   SCIENCE