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Multifaceted Hi-C benchmarking: what makes a difference in chromosome-scale genome scaffolding?

author

Mitsutaka Kadota

Osamu Nishimura

Shigehiro Kuraku

published in: GigaScience

date of publication: 2020-01-01

Cites articles 45

Date

Title

Authors

2019-08-21

Integrating Hi-C links with assembly graphs for chromosome-scale assembly

Jay Ghurye, Arang Rhie, Brian P Walenz, Mihai Pop, Adam Phillippy, Sergey Koren, Anthony P Schmitt, Siddarth Selvaraj
2019-06-05

Modern technologies and algorithms for scaffolding assembled genomes

Jay Ghurye, Mihai Pop
2019-05-01

The rising tide of high-quality genomic resources

Scott Hotaling, Joanna L. Kelley
2019-02-26

bin3C: exploiting Hi-C sequencing data to accurately resolve metagenome-assembled genomes

Matthew Z DeMaere, Aaron Earl Darling
2019-01-15

pblat: a multithread blat algorithm speeding up aligning sequences to genomes
2018-11-29

Purge Haplotigs: allelic contig reassignment for third-gen diploid genome assemblies

Michael J Roach
2018-12-01

Organizational principles of 3D genome architecture

Jordan Rowley, Victor G Corces
2018-10-08

Embryonic transcriptome sequencing of the ocellate spot skate Okamejei kenojei

Osamu Nishimura, Mitsutaka Kadota, Shigehiro Kuraku
2018-04-23

Earth BioGenome Project: Sequencing life for the future of life.

Keith A. Crandall, Scott V. Edwards, Warren E. Johnson, Erich Jarvis, Pamela S. Soltis, Igor V. Grigoriev, David Haussler, Marcus Thomas Pius Gilbert, Yang Huanming, Guojie Zhang, Richard M. Durbin, William John Baker, Jonathan A. Coddington, Félix Forest, W. John Kress, Gene E. Robinson
2018-04-11

Srf destabilizes cellular identity by suppressing cell-type-specific gene expression programs

Knut Woltjen, Kei Miyamoto, Akitsu Hotta, Takuya Yamamoto, Keisuke Okita
2018-06-01

Piercing the dark matter: bioinformatics of long-range sequencing and mapping

Fritz Sedlazeck, Hayan Lee, Charlotte A Darby
2017-11-01

gVolante for standardizing completeness assessment of genome and transcriptome assemblies

Shigehiro Kuraku, Osamu Nishimura
2017-09-05

Avian Genomes Revisited: Hidden Genes Uncovered and the Rates versus Traits Paradox in Birds.

Fidel Botero-Castro, Marie-Ka Tilak
2017-07-12

Scaffolding of long read assemblies using long range contact information

Mihai Pop, Sergey Koren, Derek M Bickhart
2017-07-10

CTCF binding landscape in jawless fish with reference to Hox cluster evolution

Wataru Takagi, Osamu Nishimura, Shigehiro Kuraku
2017-04-18

Hi-C 2.0: An optimized Hi-C procedure for high-resolution genome-wide mapping of chromosome conformation.
2017-03-23

De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds

Olga Dudchenko, Marie Hoeger, Muhammad S Shamim, Ido Machol, Eric Lander, Aviva Presser Aiden, Erez Lieberman Aiden
2016-10-01

Extraction of high-molecular-weight genomic DNA for long-read sequencing of single molecules

Jérôme Gouzy
2016-07-01

Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments

Eric Lander, Muhammad S Shamim, Erez Lieberman Aiden, Suhas S.P. Rao
2016-02-04

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

Nicholas Putnam, Daniel S. Rokhsar, David Haussler
2015-12-01

HiC-Pro: an optimized and flexible pipeline for Hi-C data processing

Nelle Varoquaux, Nicolas Servant, Emmanuel Barillot, Jean-Philippe Vert, Edith Heard
2015-06-09

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

Robert M. Waterhouse, Panagiotis Ioannidis
2015-01-01

The Genome 10K Project: a way forward

Benedict Paten
2014-12-17

High-quality genome (re)assembly using chromosomal contact data

Gianni Liti, Axel Cournac, Martial Marbouty, Romain Koszul, Nancy Guillén, Jean-François Flot, Christophe Zimmer
2014-12-11

A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping

Eric Lander, Erez Lieberman Aiden, Suhas S.P. Rao
2013-11-24

High-throughput genome scaffolding from in vivo DNA interaction frequency

Noam Kaplan
2013-11-01

Cohesin-mediated interactions organize chromosomal domain architecture

Matteo Vietri Rudan, Eitan Yaffe, Steven M Pollard, Amos Tanay
2013-11-03

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

Jay Shendure, Joshua N Burton, Jacob O Kitzman
2013-06

The draft genomes of soft-shell turtle and green sea turtle yield insights into the development and evolution of the turtle-specific body plan

Jun Wang, Kathryn Beal, Paul Flicek, Amonida Zadissa, Junyi Wang, Juan Pascual-Anaya, Qiye Li, Bronwen Aken, Javier Herrero, Guojie Zhang, Shigeru Kuratani, Naoki Irie, Shigehiro Kuraku, Simon White, Miguel Pignatelli, Steve Searle
2012-12-31

Inference of the protokaryotypes of amniotes and tetrapods and the evolutionary processes of microchromosomes from comparative gene mapping

Shigeru Kuratani, Kazumi Matsubara, Naoto Ueno, Kiyokazu Agata
2012-09-02

Iterative correction of Hi-C data reveals hallmarks of chromosome organization

Maxim Imakaev, Geoffrey Fudenberg, Anton Goloborodko, Rachel Patton McCord, Job Dekker
2012-05-29

Hi-C: a comprehensive technique to capture the conformation of genomes

Rachel Patton McCord, Job Dekker

Article - wd:Q92528454

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