Using optical mapping data for the improvement of vertebrate genome assemblies

GigaScience
Kerstin Howe, Jonathan Md Wood

Abstract

Optical mapping is a technology that gathers long-range information on genome sequences similar to ordered restriction digest maps. Because it is not subject to cloning, amplification, hybridisation or sequencing bias, it is ideally suited to the improvement of fragmented genome assemblies that can no longer be improved by classical methods. In addition, its low cost and rapid turnaround make it equally useful during the scaffolding process of de novo assembly from high throughput sequencing reads. We describe how optical mapping has been used in practice to produce high quality vertebrate genome assemblies. In particular, we detail the efforts undertaken by the Genome Reference Consortium (GRC), which maintains the reference genomes for human, mouse, zebrafish and chicken, and uses different optical mapping platforms for genome curation.

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Citations

Apr 7, 2016·Tropical Animal Health and Production·Pamela Anna Burger
May 7, 2016·Bioinformatics·William ChowKerstin Howe
Aug 31, 2016·The New Phytologist·Pär K IngvarssonNathaniel R Street
Jun 13, 2017·Bioinformatics·Yuxuan YuanDavid Edwards
Jul 25, 2017·Nature Reviews. Genetics·Jennifer R S Meadows, Kerstin Lindblad-Toh
Feb 23, 2018·Lab on a Chip·Pranav AgrawalKevin D Dorfman
Apr 25, 2018·GigaScience·José Horacio GrauMichael Hofreiter
Dec 22, 2017·Scientific Reports·Joanna M Łopacińska-JørgensenAsli Silahtaroglu
Jan 10, 2018·Frontiers in Cellular and Infection Microbiology·Jeffrey M Grabowski, Catherine A Hill
May 26, 2020·GigaScience·Heiner KuhlChristophe Klopp
Aug 18, 2020·Computational and Structural Biotechnology Journal·Yuxuan YuanTing-Fung Chan
Jan 1, 2020·Computational and Structural Biotechnology Journal·Alice Maria GianiGiulio Formenti
Feb 6, 2020·Genome Biology·Jae Young ChoiMichael D Purugganan
Apr 4, 2021·International Journal of Molecular Sciences·Mark HillsPeter M Lansdorp

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Datasets Mentioned

BETA
GM15510
GM18994

Methods Mentioned

BETA
restriction digest
whole genome shotgun

Software Mentioned

Germinate & Grow
Argus
gEVAL
OpGen Argus
Builder
BioNano Genomics
GnomSpace viewer
Irys
OpGen
Seed & Mature ( SAM

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