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Cites articles 69

Date

Title

Authors

2017-04-10

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

Sean D. McGrath, Kerstin Howe, Terence D. Murphy, Kim D. Pruitt, William Chow, Tim Hubbard, Glen Threadgold, James Torrance, Laura Clarke, Sergey Koren, Heng Li, Adam Phillippy, Paul Flicek, Deanna M. Church, Evan E. Eichler, Richard M. Durbin, Chen-Shan Chin, Milinn Kremitzki, Tina A Graves-Lindsay, Paul Peluso, Francoise Thibaud-Nissen
2016-10-17

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

Chen-Shan Chin, Fritz Sedlazeck, Christopher Dunn, Grant Cramer, Joseph R. Ecker, Dario Cantu
2016-04-01

Long-read sequence assembly of the gorilla genome

David Haussler, Katherine M Munson, Mark Diekhans, Benedict Paten, Jay Shendure, Evan E. Eichler, Christopher M Hill, Ian T Fiddes, Carl Edward Baker, Maika Malig, Mark J P Chaisson, Zev N Kronenberg, John Huddleston
2016-03-02

A time- and cost-effective strategy to sequence mammalian Y Chromosomes: an application to the de novo assembly of gorilla Y

Samarth Rangavittal, Malcolm Ferguson-Smith
2016-02-04

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

Nicholas Putnam, Daniel S. Rokhsar, David Haussler
2015-11-11

BRAKER1: Unsupervised RNA-Seq-Based Genome Annotation with GeneMark-ET and AUGUSTUS.
2015-11

Genetic variation and the de novo assembly of human genomes

Evan E. Eichler, Mark J P Chaisson
2015-06-29

Assembly and diploid architecture of an individual human genome via single-molecule technologies

Tobias Rausch, Scott C Blanchard, Chen-Shan Chin, Jan Korbel, Oscar Franzén, Robert Sebra, Gintaras Deikus, Christopher E. Mason, Eric E Schadt
2015-06-09

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

Robert M. Waterhouse, Panagiotis Ioannidis
2015-05-25

Assembling large genomes with single-molecule sequencing and locality-sensitive hashing

Chen-Shan Chin, Sergey Koren, Adam Phillippy
2015-02-18

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

Steven Salzberg, Mihaela Pertea
2014-12-11

Comparative genomic data of the Avian Phylogenomics Project

Guojie Zhang, Cai Li, Marcus Thomas Pius Gilbert, Erich Jarvis, Jun Wang
2014-11-19

Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement

Thomas Abeel, Christina A Cuomo, Ashlee Earl, Jennifer R Wortman
2014-12-15

Definition of the cattle killer cell Ig-like receptor gene family: comparison with aurochs and human counterparts

Andrew Warry, Paul J Norman, Mick Watson, David E. MacHugh, Daniel G. Bradley, Nicholas Sanderson, Matthew Breen, Lisbeth A Guethlein
2014-09-04

Illumina TruSeq synthetic long-reads empower de novo assembly and resolve complex, highly-repetitive transposable elements

Rajiv C. McCoy, Joanna L. Kelley, Dmitri A. Petrov, Anna-Sophie Fiston-Lavier
2014-06-26

LUMPY: a probabilistic framework for structural variant discovery

Colby Chiang, Aaron R Quinlan
2014-06-20

SSPACE-LongRead: scaffolding bacterial draft genomes using long read sequence information
2014-05-22

Species-level deconvolution of metagenome assemblies with Hi-C-based contact probability maps

Jay Shendure, Maitreya Dunham
2014-08

Analysis of 41 plant genomes supports a wave of successful genome duplications in association with the Cretaceous-Paleogene boundary

Guy Baele, Yves Van de Peer, Steven Maere
2014-04-01

Trimmomatic: a flexible trimmer for Illumina sequence data

Björn Usadel, Anthony M. Bolger
2014-03-03

Kraken: ultrafast metagenomic sequence classification using exact alignments

Derrick E Wood, Steven Salzberg
2014-01-22

Design and characterization of a 52K SNP chip for goats

Jun Wang, Gwenola Tosser-Klopp, International Goat Genome Consortium, Isabelle Palhière, Eric Pailhoux, Gwenola Tosser-Klopp, John C. McEwan, Christophe Klopp, Richard P. M. A. Crooijmans
2014-12-01

Fine-scale chromatin interaction maps reveal the cis-regulatory landscape of human lincRNA genes

Jay Shendure, Wenxiu Ma, Ferhat Ay, Gunhan Gulsoy, Christine Disteche
2013-11-24

High-throughput genome scaffolding from in vivo DNA interaction frequency

Noam Kaplan
2013-11-03

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

Jay Shendure, Joshua N Burton, Jacob O Kitzman
2013-11-03

Whole-genome haplotype reconstruction using proximity-ligation and shotgun sequencing
2013-01-01

Reducing assembly complexity of microbial genomes with single-molecule sequencing

Sergey Koren, Adam Phillippy, Nicholas H. Bergman, Gregory P Harhay, James L Bono, Dayna M Harhay
2013-06-11

Comprehensive genotyping of the USA national maize inbred seed bank

Edward Buckler, Cinta Romay, Kelly L Swarts, Terry Casstevens, Robert J Elshire, Sherry Flint-Garcia, Jim Holland
2013-05-29

Characterizing and measuring bias in sequence data

Carsten Russ, Maura Costello, Chad Nusbaum
2013-06

Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data
2013

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

Harold Pimentel, Steven Salzberg, Cole Trapnell
2013-02-06

Rapid genome mapping in nanochannel arrays for highly complete and accurate de novo sequence assembly of the complex Aegilops tauschii genome.

Pui-Yan Kwok, Ming-Cheng Luo, Jan Dvorak

Article - wd:Q40306687

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