Table of Contents

Editorial

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New advances in sequence assembly
- Adam M. Phillippy
Genome Res. May 2017 27: xi-xiii; doi:10.1101/gr.223057.117
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Review

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Genome graphs and the evolution of genome inference
- Benedict Paten,
- Adam M. Novak,
- Jordan M. Eizenga,
- and Erik Garrison
Genome Res. May 2017 27: 665-676; Published in Advance March 30, 2017, doi:10.1101/gr.214155.116
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Research

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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,
- Chen-Shin Chin,
- Jonas Korlach,
- Richard K. Wilson,
- and Evan E. Eichler
Genome Res. May 2017 27: 677-685; Published in Advance November 28, 2016, doi:10.1101/gr.214007.116
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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 II,
- Cathy Gresham,
- Fiona McCarthy,
- Colin Kern,
- David Haan,
- Tan Phan,
- Carl Schmidt,
- Jeremy R. Sanford,
- David A. Ray,
- Benedict Paten,
- Louis J. Guillette, Jr.,
- and Richard E. Green
Genome Res. May 2017 27: 686-696; Published in Advance January 30, 2017, doi:10.1101/gr.213595.116
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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,
- Alexander Suh,
- and Jochen B.W. Wolf
Genome Res. May 2017 27: 697-708; Published in Advance March 30, 2017, doi:10.1101/gr.215095.116
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Single-molecule sequencing resolves the detailed structure of complex satellite DNA loci in Drosophila melanogaster
- Daniel E. Khost,
- Danna G. Eickbush,
- and Amanda M. Larracuente
Genome Res. May 2017 27: 709-721; Published in Advance April 3, 2017, doi:10.1101/gr.213512.116
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Resources

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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,
- Richard K. Wilson,
- Paul Flicek,
- Evan E. Eichler,
- and Deanna M. Church
Genome Res. May 2017 27: 849-864; Published in Advance April 10, 2017, doi:10.1101/gr.213611.116
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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,
- Shuhong Zhao,
- Jinyong Wang,
- Ruiqiang Li,
- and Xuewei Li
Genome Res. May 2017 27: 865-874; Published in Advance September 19, 2016, doi:10.1101/gr.207456.116
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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,
- Sunitha Joseph,
- Martin T. Swain,
- Darren K. Griffin,
- and Denis M. Larkin
Genome Res. May 2017 27: 875-884; Published in Advance November 30, 2016, doi:10.1101/gr.213660.116
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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,
- Ksenia V. Krasileva,
- David Swarbreck,
- Michael W. Bevan,
- and Matthew D. Clark
Genome Res. May 2017 27: 885-896; Published in Advance April 18, 2017, doi:10.1101/gr.217117.116
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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

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