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Highly accurate assembly polishing with DeepPolisher

Mira Mastoras
Mobin Asri
Lucas Brambrink
Prajna Hebbar
Alexey Kolesnikov
Daniel E. Cook Maria Nattestad Julian Lucas Taylor S. Won Pi-Chuan Chang Andrew Carroll Benedict Paten Kishwar Shafin Ahmad Abou Tayoun Derek Albracht Jamie Allen Alawi A. Alsheikh-Ali Casey Andrews Dmitry Antipov Lucinda Antonacci-Fulton Mobin Asri Marcelo Ayllon Jennifer R. Balacco Edward A. Belter Halle D. Bender Andrew P. Blair Silvia Buonaiuto Davide Bolognini Katherine E. Bonini Christina Boucher Guillaume Bourque Shuo Cao Andrew Carroll Ann M. Mc Cartney Monika Cechova Pi-Chuan Chang Xian Chang Jitender Cheema Haoyu Cheng Claudio Ciofi Sarah Cody Vincenza Colonna Holland C. Conwell Robert Cook-Deegan Mark Diekhans Maria Angela Diroma Daniel Doerr Zheng Dong Richard Durbin Jana Ebler Evan E Eichler Jordan M. Eizenga Parsa Eskandar Eddie Ferro Anna-Sophie Fiston-Lavier Sarah M. Ford Willard W. Ford Giulio Formenti Adam Frankish Mallory A. Freeberg Qichen Fu Stephanie M. Fullerton Robert S. Fulton Yan Gao Gage H. Garcia Obed A. Garcia Joshua M.V. Gardner Shilpa Garg Erik Garrison Nanibaa' A. Garrison John Garza Mohammadmersad Ghorbani Tina Graves-Lindsay Richard E. Green Cristian Groza Andrea Guarracino Melissa Gymrek Leanne Haggerty Ira M. Hall Nancy F. Hansen Mohammad Amiruddin Hashmi Maximilian Haeussler David Haussler Prajna Hebbar Peter Heringer Glenn Hickey Todd L. Hillaker S. Nakib Hossain Neng Huang Sarah E. Hunt Toby Hunt Nafiseh Jafarzadeh Nivesh Jain Erich D. Jarvis Juan Jiang Jonathan LoTempio Eimear E. Kenny Juhyun Kim Bonhwang Koo Sergey Koren Milinn Kremitzki Ben Langmead Xiaoyu Zhuo Heather A. Lawson Daofeng Li Heng Li Wen-Wei Liao Jiadong Lin Tianjie Liu Glennis A. Logsdon Ryan Lorig-Roach Hailey Loucks Jane E. Loveland Jianguo Lu Shuangjia Lu Julian K. Lucas Juan F. Macias-Velasco Maximillian G. Marin Franco L. Marsico Kateryna D. Makova Christopher Markovic Tobias Marschall Fergal J. Martin Mira Mastoras Capucine Mayoud Brandy McNulty Jack A. Medico Julian M. Menendez Karen H. Miga Anna Minkina Matthew W. Mitchell Saswat K. Mohanty Younes Mokrab Jean Monlong Shabir Moosa Avelina Moreno-Ochando Shinichi Morishita Jonathan M. Mudge Katherine M. Munson Njagi Mwaniki Nasna Nassir Chiara Natali Shloka Negi Lingbin Ni Adam M. Novak Chie Owa Sadye Paez Benedict Paten Hiram Clawson Clelia Peano Adam M. Phillippy Brandon D. Pickett Laura Pignata Nadia Pisanti David Porubsky Pjotr Prins Anandi Radhakrishnan Brian J. Raney Mikko Rautiainen Alessandro Raveane Luyao Ren Arang Rhie Farnaz Salehi Samuel Sacco Michael C. Schatz Laura B. Scheinfeldt Aarushi Sehgal William E. Seligmann Mahsa Shabani Kishwar Shafin Shadi Shahatit Ruhollah Shemirani Vikram S. Shivakumar Swati Sinha Jouni Sirén Linnéa Smeds Steven J. Solar Marco Sollitto Nicole Soranzo Andrew B. Stergachis Marie-Marthe Suner Yoshihiko Suzuki Arda Söylev Jack A.S. Tierney Chad Tomlinson Francesca Floriana Tricomi Mohammed Uddin Matteo Tommaso Ungaro Rahul Varki Flavia Villani Mitchell R. Vollger Brian P. Walenz Charles Wang Lisa E. Wang Ting Wang Aaron M. Wenger Conor V. Whelan Zilan Xin Zheng Xu Kai Ye DongAhn Yoo
... [+196 authors] ...,
Wenjin Zhang
Ying Zhou
Ivo Violich
Giulia Zunino

First Published May 19, 2025

Lake Malawi cichlid pangenome graph reveals extensive structural variation driven by transposable elements

Fu Xiang Quah
Miguel Vasconcelos Almeida
Moritz Blumer
Chengwei Ulrika Yuan
Bettina Fischer
Kirsten See Ben Jackson Richard Zatha Bosco Rusuwa George F. Turner M. Emília Santos
... [+6 authors] ...,
Hannes Svardal
Martin Hemberg
Richard Durbin
Eric Miska

First Published April 10, 2025

MCHelper automatically curates transposable element libraries across eukaryotic species

Simon Orozco-Arias
Pío Sierra
Richard Durbin
Josefa González

First Published December 9, 2024

Ultrafast genome-wide inference of pairwise coalescence times

Regev Schweiger
Richard Durbin

First Published August 10, 2023

Diversity, duplication, and genomic organization of homeobox genes in Lepidoptera

Peter O. Mulhair
Liam Crowley
Douglas H. Boyes
Amber Harper
Owen T. Lewis
Peter W.H. Holland Mark Blaxter Nova Mieszkowska Federica Di Palma Peter Holland Richard Durbin Thomas Richards Matthew Berriman Paul Kersey Peter Hollingsworth Willie Wilson Alex Twyford Ester Gaya Mara Lawniczak Owen Lewis Gavin Broad
... [+16 authors] ...,
Kevin Howe
Michelle Hart
Paul Flicek
Ian Barnes

First Published December 8, 2022

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

Using reference-free compressed data structures to analyze sequencing reads from thousands of human genomes

Dirk D. Dolle
Zhicheng Liu
Matthew Cotten
Jared T. Simpson
Zamin Iqbal
Richard Durbin
Shane A. McCarthy
Thomas M. Keane

First Published December 16, 2016

Efficient de novo assembly of large genomes using compressed data structures

Jared T. Simpson
Richard Durbin

First Published December 7, 2011

Assemblathon 1: A competitive assessment of de novo short read assembly methods

Dent Earl
Keith Bradnam
John St. John
Aaron Darling
Dawei Lin
Joseph Fass Hung On Ken Yu Vince Buffalo Daniel R. Zerbino Mark Diekhans Ngan Nguyen Pramila Nuwantha Ariyaratne Wing-Kin Sung Zemin Ning Matthias Haimel Jared T. Simpson Nuno A. Fonseca İnanç Birol T. Roderick Docking Isaac Y. Ho Daniel S. Rokhsar Rayan Chikhi Dominique Lavenier Guillaume Chapuis Delphine Naquin Nicolas Maillet Michael C. Schatz David R. Kelley Adam M. Phillippy Sergey Koren Shiaw-Pyng Yang Wei Wu Wen-Chi Chou Anuj Srivastava Timothy I. Shaw J. Graham Ruby Peter Skewes-Cox Miguel Betegon Michelle T. Dimon Victor Solovyev Igor Seledtsov Petr Kosarev Denis Vorobyev Ricardo Ramirez-Gonzalez Richard Leggett Dan MacLean Fangfang Xia Ruibang Luo Zhenyu Li Yinlong Xie Binghang Liu Sante Gnerre Iain MacCallum Dariusz Przybylski Filipe J. Ribeiro Shuangye Yin Ted Sharpe Giles Hall Paul J. Kersey Richard Durbin Shaun D. Jackman Jarrod A. Chapman Xiaoqiu Huang Joseph L. DeRisi Mario Caccamo Yingrui Li David B. Jaffe
... [+62 authors] ...,
Richard E. Green
David Haussler
Ian Korf
Benedict Paten

First Published September 16, 2011

Revealing the genetic structure of a trait by sequencing a population under selection

Leopold Parts
Francisco A. Cubillos
Jonas Warringer
Kanika Jain
Francisco Salinas
Suzannah J. Bumpstead Mikael Molin Amin Zia Jared T. Simpson Michael A. Quail
... [+5 authors] ...,
Alan Moses
Edward J. Louis
Richard Durbin
Gianni Liti

First Published March 21, 2011

Dindel: Accurate indel calls from short-read data

Cornelis A. Albers
Gerton Lunter
Daniel G. MacArthur
Gilean McVean
Willem H. Ouwehand
Richard Durbin

First Published October 27, 2010

SNP detection and genotyping from low-coverage sequencing data on multiple diploid samples

Si Quang Le
Richard Durbin

First Published October 27, 2010

The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes

Kim D. Pruitt
Jennifer Harrow
Rachel A. Harte
Craig Wallin
Mark Diekhans
Donna R. Maglott Steve Searle Catherine M. Farrell Jane E. Loveland Barbara J. Ruef Elizabeth Hart Marie-Marthe Suner Melissa J. Landrum Bronwen Aken Sarah Ayling Robert Baertsch Julio Fernandez-Banet Joshua L. Cherry Val Curwen Michael DiCuccio Manolis Kellis Jennifer Lee Michael F. Lin Michael Schuster Andrew Shkeda Clara Amid Garth Brown Oksana Dukhanina Adam Frankish Jennifer Hart Bonnie L. Maidak Jonathan Mudge Michael R. Murphy Terence Murphy Jeena Rajan Bhanu Rajput Lillian D. Riddick Catherine Snow Charles Steward David Webb Janet A. Weber Laurens Wilming Wenyu Wu Ewan Birney David Haussler
... [+40 authors] ...,
Tim Hubbard
James Ostell
Richard Durbin
David Lipman

First Published June 4, 2009

EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates

Albert J. Vilella
Jessica Severin
Abel Ureta-Vidal
Li Heng
Richard Durbin
Ewan Birney

First Published November 24, 2008

Mapping short DNA sequencing reads and calling variants using mapping quality scores

Heng Li
Jue Ruan
Richard Durbin

First Published August 19, 2008

GeneWise and Genomewise

Ewan Birney
Michele Clamp
Richard Durbin

First Published May 3, 2004

An Overview of Ensembl

Ewan Birney
T. Daniel Andrews
Paul Bevan
Mario Caccamo
Yuan Chen
Laura Clarke Guy Coates James Cuff Val Curwen Tim Cutts Thomas Down Eduardo Eyras Xose M. Fernandez-Suarez Paul Gane Brian Gibbins James Gilbert Martin Hammond Hans-Rudolf Hotz Vivek Iyer Kerstin Jekosch Andreas Kahari Arek Kasprzyk Damian Keefe Stephen Keenan Heikki Lehvaslaiho Graham McVicker Craig Melsopp Patrick Meidl Emmanuel Mongin Roger Pettett Simon Potter Glenn Proctor Mark Rae Steve Searle Guy Slater Damian Smedley James Smith Will Spooner Arne Stabenau James Stalker Roy Storey Abel Ureta-Vidal K. Cara Woodwark Graham Cameron
... [+39 authors] ...,
Richard Durbin
Anthony Cox
Tim Hubbard
Michele Clamp

First Published April 12, 2004

Locating Sequence on FPC Maps and Selecting a Minimal Tiling Path

Friedrich W. Engler
James Hatfield
William Nelson
Carol A. Soderlund

First Published January 1, 2003

GAZE: A Generic Framework for the Integration of Gene-Prediction Data by Dynamic Programming

Kevin L. Howe
Tom Chothia
Richard Durbin

First Published September 1, 2002

Alfresco—A Workbench for Comparative Genomic Sequence Analysis

Niclas Jareborg
Richard Durbin

First Published August 1, 2000

GeneWise in the Drosophila Annotation Experiment" > Using `GeneWise` in the Drosophila Annotation Experiment

Ewan Birney
Richard Durbin

First Published April 1, 2000

Comparative Analysis of Noncoding Regions of 77 Orthologous Mouse and Human Gene Pairs

Niclas Jareborg
Ewan Birney
Richard Durbin

First Published September 1, 1999

Sequence Assembly with CAFTOOLS

Simon Dear
Richard Durbin
LaDeana Hillier
Gabor Marth
Jean Thierry-Mieg
Richard Mott

First Published March 1, 1998

Base Qualities Help Sequencing Software

Richard Durbin
Simon Dear

First Published March 1, 1998

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Your search for returned 24 results

Highly accurate assembly polishing with DeepPolisher

Lake Malawi cichlid pangenome graph reveals extensive structural variation driven by transposable elements

MCHelper automatically curates transposable element libraries across eukaryotic species

Ultrafast genome-wide inference of pairwise coalescence times

Diversity, duplication, and genomic organization of homeobox genes in Lepidoptera

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

Using reference-free compressed data structures to analyze sequencing reads from thousands of human genomes

Efficient de novo assembly of large genomes using compressed data structures

Assemblathon 1: A competitive assessment of de novo short read assembly methods

Revealing the genetic structure of a trait by sequencing a population under selection

Dindel: Accurate indel calls from short-read data

SNP detection and genotyping from low-coverage sequencing data on multiple diploid samples

The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes

EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates

Mapping short DNA sequencing reads and calling variants using mapping quality scores

GeneWise and Genomewise

An Overview of Ensembl

Locating Sequence on FPC Maps and Selecting a Minimal Tiling Path

GAZE: A Generic Framework for the Integration of Gene-Prediction Data by Dynamic Programming

Alfresco—A Workbench for Comparative Genomic Sequence Analysis

GeneWise in the Drosophila Annotation Experiment" > Using `GeneWise` in the Drosophila Annotation Experiment

Comparative Analysis of Noncoding Regions of 77 Orthologous Mouse and Human Gene Pairs

Sequence Assembly with CAFTOOLS

Base Qualities Help Sequencing Software

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Your search for returned 24 results