Volume 27, Issue 5 | May 2017

Editorial
- - New advances in sequence assembly
    Adam M. Phillippy
    First Published May 1, 2017
Review
- - Genome graphs and the evolution of genome inference
    Benedict Paten
    Adam M. Novak
    Jordan M. Eizenga
    Erik Garrison
    First Published March 30, 2017
Research
- - Discovery and genotyping of structural variation from long-read haploid genome sequence data
    John Huddleston
    Mark J.P. Chaisson
    Karyn Meltz Steinberg
    Wes Warren
    Kendra Hoekzema
    David Gordon Tina A. Graves-Lindsay Katherine M. Munson Zev N. Kronenberg Laura Vives Paul Peluso Matthew Boitano
    ...[+7 authors]...,
    Chen-Shin Chin
    Jonas Korlach
    Richard K. Wilson
    Evan E. Eichler
    First Published November 28, 2016
  - Improved genome assembly of American alligator genome reveals conserved architecture of estrogen signaling
    Edward S. Rice
    Satomi Kohno
    John St. John
    Son Pham
    Jonathan Howard
    Liana F. Lareau Brendan L. O'Connell Glenn Hickey Joel Armstrong Alden Deran Ian Fiddes Roy N. Platt Cathy Gresham Fiona McCarthy Colin Kern David Haan Tan Phan Carl Schmidt Jeremy R. Sanford
    ...[+14 authors]...,
    David A. Ray
    Benedict Paten
    Louis J. Guillette
    Richard E. Green
    First Published January 30, 2017
  - Combination of short-read, long-read, and optical mapping assemblies reveals large-scale tandem repeat arrays with population genetic implications
    Matthias H. Weissensteiner
    Andy W.C. Pang
    Ignas Bunikis
    Ida Höijer
    Olga Vinnere-Petterson
    First Published March 30, 2017
  - Single-molecule sequencing resolves the detailed structure of complex satellite DNA loci in Drosophila melanogaster
    Daniel E. Khost
    Danna G. Eickbush
    Amanda M. Larracuente
    First Published April 3, 2017
Methods
- - Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation
    Sergey Koren
    Brian P. Walenz
    Konstantin Berlin
    Jason R. Miller
    Nicholas H. Bergman
    First Published March 15, 2017
  - Fast and accurate de novo genome assembly from long uncorrected reads
    Robert Vaser
    Ivan Sović
    Niranjan Nagarajan
    Mile Šikić
    First Published January 18, 2017
  - HINGE: long-read assembly achieves optimal repeat resolution
    Govinda M. Kamath
    Ilan Shomorony
    Fei Xia
    Thomas A. Courtade
    David N. Tse
    First Published March 20, 2017
  - Direct determination of diploid genome sequences
    Neil I. Weisenfeld
    Vijay Kumar
    Preyas Shah
    Deanna M. Church
    David B. Jaffe
    First Published April 5, 2017
  - ABySS 2.0: resource-efficient assembly of large genomes using a Bloom filter
    Shaun D. Jackman
    Benjamin P. Vandervalk
    Hamid Mohamadi
    Justin Chu
    Sarah Yeo
    S. Austin Hammond Golnaz Jahesh
    ...[+2 authors]...,
    Hamza Khan
    Lauren Coombe
    Rene L. Warren
    Inanc Birol
    First Published February 23, 2017
  - Improving and correcting the contiguity of long-read genome assemblies of three plant species using optical mapping and chromosome conformation capture data
    Wen-Biao Jiao
    Gonzalo Garcia Accinelli
    Benjamin Hartwig
    Christiane Kiefer
    David Baker
    Edouard Severing Eva-Maria Willing Mathieu Piednoel Stefan Woetzel Eva Madrid-Herrero Bruno Huettel Ulrike Hümann Richard Reinhard Marcus A. Koch
    ...[+9 authors]...,
    Daniel Swan
    Bernardo Clavijo
    George Coupland
    Korbinian Schneeberger
    First Published February 3, 2017
  - Hybrid assembly of the large and highly repetitive genome of Aegilops tauschii, a progenitor of bread wheat, with the MaSuRCA mega-reads algorithm
    Aleksey V. Zimin
    Daniela Puiu
    Ming-Cheng Luo
    Tingting Zhu
    Sergey Koren
    First Published January 27, 2017
  - HySA: a Hybrid Structural variant Assembly approach using next-generation and single-molecule sequencing technologies
    Xian Fan
    Mark Chaisson
    Luay Nakhleh
    Ken Chen
    First Published January 19, 2017
  - HapCUT2: robust and accurate haplotype assembly for diverse sequencing technologies
    Peter Edge
    Vineet Bafna
    Vikas Bansal
    First Published December 9, 2016
  - Sequences of 95 human MHC haplotypes reveal extreme coding variation in genes other than highly polymorphic HLA class I and II
    Paul J. Norman
    Steven J. Norberg
    Lisbeth A. Guethlein
    Neda Nemat-Gorgani
    Thomas Royce
    Emily E. Wroblewski Tamsen Dunn Tobias Mann Claudia Alicata Jill A. Hollenbach Weihua Chang Melissa Shults Won
    ...[+7 authors]...,
    Kevin L. Gunderson
    Laurent Abi-Rached
    Mostafa Ronaghi
    Peter Parham
    First Published March 30, 2017
  - metaSPAdes: a new versatile metagenomic assembler
    Sergey Nurk
    Dmitry Meleshko
    Anton Korobeynikov
    Pavel A. Pevzner
    First Published March 15, 2017
  - De novo assembly of viral quasispecies using overlap graphs
    Jasmijn A. Baaijens
    Amal Zine El Aabidine
    Eric Rivals
    Alexander Schönhuth
    First Published April 10, 2017
Resources
- - Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly
    Valerie A. Schneider
    Tina Graves-Lindsay
    Kerstin Howe
    Nathan Bouk
    Hsiu-Chuan Chen
    Paul A. Kitts Terence D. Murphy Kim D. Pruitt Françoise Thibaud-Nissen Derek Albracht Robert S. Fulton Milinn Kremitzki Vincent Magrini Chris Markovic Sean McGrath Karyn Meltz Steinberg Kate Auger William Chow Joanna Collins Glenn Harden Timothy Hubbard Sarah Pelan Jared T. Simpson Glen Threadgold James Torrance Jonathan M. Wood Laura Clarke Sergey Koren Matthew Boitano Paul Peluso Heng Li Chen-Shan Chin Adam M. Phillippy Richard Durbin
    ...[+29 authors]...,
    Richard K. Wilson
    Paul Flicek
    Evan E. Eichler
    Deanna M. Church
    First Published April 10, 2017
  - Comprehensive variation discovery and recovery of missing sequence in the pig genome using multiple de novo assemblies
    Mingzhou Li
    Lei Chen
    Shilin Tian
    Yu Lin
    Qianzi Tang
    Xuming Zhou Diyan Li Carol K.L. Yeung Tiandong Che Long Jin Yuhua Fu Jideng Ma Xun Wang Anan Jiang Jing Lan Qi Pan Yingkai Liu Zonggang Luo Zongyi Guo Haifeng Liu Li Zhu Surong Shuai Guoqing Tang Jiugang Zhao Yanzhi Jiang Lin Bai Shunhua Zhang Miaomiao Mai Changchun Li Dawei Wang Yiren Gu Guosong Wang Hongfeng Lu Yan Li Haihao Zhu Zongwen Li Ming Li Vadim N. Gladyshev Zhi Jiang
    ...[+34 authors]...,
    Shuhong Zhao
    Jinyong Wang
    Ruiqiang Li
    Xuewei Li
    First Published September 19, 2016
  - Upgrading short-read animal genome assemblies to chromosome level using comparative genomics and a universal probe set
    Joana Damas
    Rebecca O'Connor
    Marta Farré
    Vasileios Panagiotis E. Lenis
    Henry J. Martell
    Anjali Mandawala Katie Fowler
    ...[+2 authors]...,
    Sunitha Joseph
    Martin T. Swain
    Darren K. Griffin
    Denis M. Larkin
    First Published November 30, 2016
  - An improved assembly and annotation of the allohexaploid wheat genome identifies complete families of agronomic genes and provides genomic evidence for chromosomal translocations
    Bernardo J. Clavijo
    Luca Venturini
    Christian Schudoma
    Gonzalo Garcia Accinelli
    Gemy Kaithakottil
    Jonathan Wright Philippa Borrill George Kettleborough Darren Heavens Helen Chapman James Lipscombe Tom Barker Fu-Hao Lu Neil McKenzie Dina Raats Ricardo H. Ramirez-Gonzalez Aurore Coince Ned Peel Lawrence Percival-Alwyn Owen Duncan Josua Trösch Guotai Yu Dan M. Bolser Guy Namaati Arnaud Kerhornou Manuel Spannagl Heidrun Gundlach Georg Haberer Robert P. Davey Christine Fosker Federica Di Palma Andrew L. Phillips A. Harvey Millar Paul J. Kersey Cristobal Uauy
    ...[+30 authors]...,
    Ksenia V. Krasileva
    David Swarbreck
    Michael W. Bevan
    Matthew D. Clark
    First Published April 18, 2017

Table of Contents

Volume 27, Issue 5 | May 2017

Editorial

New advances in sequence assembly

Review

Genome graphs and the evolution of genome inference

Research

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

Improved genome assembly of American alligator genome reveals conserved architecture of estrogen signaling

Combination of short-read, long-read, and optical mapping assemblies reveals large-scale tandem repeat arrays with population genetic implications

Single-molecule sequencing resolves the detailed structure of complex satellite DNA loci in Drosophila melanogaster

Methods

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

Fast and accurate de novo genome assembly from long uncorrected reads

HINGE: long-read assembly achieves optimal repeat resolution

Direct determination of diploid genome sequences

ABySS 2.0: resource-efficient assembly of large genomes using a Bloom filter

Improving and correcting the contiguity of long-read genome assemblies of three plant species using optical mapping and chromosome conformation capture data

Hybrid assembly of the large and highly repetitive genome of Aegilops tauschii, a progenitor of bread wheat, with the MaSuRCA mega-reads algorithm

HySA: a Hybrid Structural variant Assembly approach using next-generation and single-molecule sequencing technologies

HapCUT2: robust and accurate haplotype assembly for diverse sequencing technologies

Sequences of 95 human MHC haplotypes reveal extreme coding variation in genes other than highly polymorphic HLA class I and II

metaSPAdes: a new versatile metagenomic assembler

De novo assembly of viral quasispecies using overlap graphs

Resources

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

Comprehensive variation discovery and recovery of missing sequence in the pig genome using multiple de novo assemblies

Upgrading short-read animal genome assemblies to chromosome level using comparative genomics and a universal probe set

An improved assembly and annotation of the allohexaploid wheat genome identifies complete families of agronomic genes and provides genomic evidence for chromosomal translocations

Table of Contents

Volume 27, Issue 5 | May 2017

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Editorial

Review

Research

Methods

Resources