Next-generation sequencing and large genome assemblies

Keywords

DNA sequencing, Sequence assembly, Computational biology, Genome, Hybrid genome assembly

References

• ALLPATHS: de novo assembly of whole-genome shotgun microreads.Van Loenen, Berry Leanne — 2008
• Genome sequencing and assembly.Manfred Grabherr, Evan Mauceli, Li‐Jun Ma — 2011
• A whole-genome assembly of Drosophila.Eugene W. Myers, Granger G. Sutton, Art L. Delcher — 2000
• Structural variation in two human genomes mapped at single-nucleotide resolution by whole genome de novo assemblyYingrui Li, Hancheng Zheng, Ruibang Luo — 2011
• Genomic mapping by fingerprinting random clones: a mathematical analysis.Eric S. Lander, Michael S. Waterman — 1988
• ABySS: a parallel assembler for short read sequence data.Jared T. Simpson, Kim Wong, Shaun D. Jackman — 2009
• SOPRA: Scaffolding algorithm for paired reads via statistical optimizationAdel Dayarian, Todd P. Michael, Anirvan M. Sengupta — 2010
• Accuracy and quality assessment of 454 GS-FLX Titanium pyrosequencingAndré Gilles, Emese Meglécz, Nicolas Pech — 2011
• Pebble and Rock Band: Heuristic Resolution of Repeats and Scaffolding in the Velvet Short-Read de Novo AssemblerDaniel R. Zerbino, Gayle K. McEwen, Elliott H. Margulies — 2009
• Utilization of next-generation sequencing platforms in plant genomics and genetic variant discoveryStéphane Deschamps, Matthew A. Campbell — 2010
• An integrated semiconductor device enabling non-optical genome sequencingJonathan M. Rothberg, Wolfgang Hinz, Todd M. Rearick — 2011
• The diploid genome sequence of an Asian individualJun Wang, Wei Wang, Ruiqiang Li — 2008
• Next-generation sequencing of vertebrate experimental organismsDaniel J. Turner, Thomas Keane, Ian Sudbery — 2009
• De novo assembly and genotyping of variants using colored de Bruijn graphsZamin Iqbal, Mario Cáccamo, Isaac Turner — 2012
• High-quality draft assemblies of mammalian genomes from massively parallel sequence dataSante Gnerre, Iain MacCallum, Dariusz Przybylski — 2010
• Illumina mate-paired DNA sequencing-library preparation using Cre-Lox recombinationFilip Van Nieuwerburgh, Ryan C. Thompson, Jessica Ledesma — 2011
• Generation of Long Insert Pairs Using a Cre-LoxP Inverse PCR ApproachZe Peng, Zhiying Zhao, Nandita Nath — 2012
• The power of NGS technologies to delineate the genome organization in cancer: from mutations to structural variations and epigenetic alterationsMichal R. Schweiger, Martin Kerick, Bernd Timmermann — 2011
• Limitations of next-generation genome sequence assemblyCan Alkan, Saba Sajjadian, Evan E. Eichler — 2010
• Complete Khoisan and Bantu genomes from southern AfricaStephan C. Schuster, Webb Miller, Aakrosh Ratan — 2010

Cited by

• Validation and assessment of variant calling pipelines for next-generation sequencing誠 米山, 貞利 目黒, 進策 河内 — 2014
• A pipeline for local assembly of minisatellite alleles from single-molecule sequencing data健一 大串, 直樹 根本 — 2016
• A Primer on Infectious Disease Bacterial GenomicsС М Грігор’єв, В І Іванов, Т М Нестеренко — 2016
• SMRT long reads and Direct Label and Stain optical maps allow the generation of a high-quality genome assembly for the European barn swallow (Hirundo rustica rustica)Richard A. Epstein — 2018
• Fuzzy k-mers and their application to comparative genome assemblyJohn Healy — 2013
• Network Algorithms for Complex Systems with Applications to Non-linear Oscillators and Genome AssemblyKarl R. B. Schmitt — 2013
• The integration of sequencing and bioinformatics in metagenomicsFirouz Abbasian, Robin Lockington, Mallavarapu Megharaj — 2015
• Data Mining Techniques for the Life SciencesOliviero Carugo, Frank Eisenhaber — 2009
• Next-generation sequencing in clinical virology: Discovery of new viruses.Sibnarayan Datta — 2015
• A Genomic and Proteomic Investigation of the Plant Pathogen Armillaria mellea: Buried Treasure or Hidden Threat?Collins Cassandra — 2013
• A hierarchical network heuristic for solving the orientation problem in genome assemblyKarl R. B. Schmitt, Aleksey V. Zimin, Guillaume Marcaçs — 2013
• IMPROVING EUKARYOTIC GENOME ASSEMBLY THROUGH APPLICATION OF SINGLE MOLECULE REAL-TIME SEQUENCING DATA GENOME: COFFEE LEAF RUST FUNGUS, H. vastatrixModupeore O. Adetunji — 2014
• Sequencing and de novo draft assemblies of a fathead minnow (Pimephales promelas) reference genomeFrank Burns, Amarin Cogburn, Gerald T. Ankley — 2016
• Cardiovascular genetics: technological advancements and applicability for dilated cardiomyopathyGijs J.M. Kummeling, Annette F. Baas, Magdaléna Harakaľová — 2015
• Investigating the genetics and pharmacogenetics of bowel cancerHannah D. West — 2013
• The study of biodiversity in the era of massive sequencingAna E. Escalante, Lev Jardón‐Barbolla, Santiago Ramírez‐Barahona — 2014
• Challenges and Opportunities of Airborne MetagenomicsHayedeh Behzad, Takashi Gojobori, Katsuhiko Mineta — 2015
• (Post-)genomics approaches in fungal research.María Victoria Aguilar Pontes, Ronald P. de Vries, Miaomiao Zhou — 2014
• RNA-Seq Analysis of the Response of the Halophyte, Mesembryanthemum crystallinum (Ice Plant) to High SalinityHironaka Tsukagoshi, Takamasa Suzuki, Kouki Nishikawa — 2015
• Proteomics of nonmodel plant speciesAntoine Champagne, Marc Boutry — 2013

Related papers

• Identification of Optimum Sequencing Depth Especially for De Novo Genome Assembly of Small Genomes Using Next Generation Sequencing DataAarti Desai, Veer Singh Marwah, Akshay R. Yadav — 2013
• GAGE: A critical evaluation of genome assemblies and assembly algorithms.Steven L. Salzberg, Adam M. Phillippy, Aleksey V. Zimin — 2012
• Efficient and highly continuous chromosome-level genome assembly of a diploid amniote genomeHong‐Xin Xie, Zixuan Chen, Shuai Pang — 2023
• Comparative genome assemblyMihai Pop — 2004
• Rapid Genome Mapping in Nanochannel Arrays for Highly Complete and Accurate De Novo Sequence Assembly of the Complex Aegilops tauschii GenomeAlex Hastie, Lingli Dong, Alexis L. Smith — 2013
• Approaches to DNA de novo assemblyIvan Sović, Karolj Skala, Mile Šikić — 2013