De Novo Assembly of a New Solanum pennellii Accession Using Nanopore Sequencing.
Maximilian Schmidt,Alexander Vogel,Alisandra K. Denton,Benjamin Istace,Alexandra Wormit,Henri van de Geest,Marie E. Bolger,Saleh Alseekh,Janina Maß,Christian Pfaff,Ulrich Schurr,Roger T. Chetelat,Florian Maumus,Jean-Marc Aury,Sergey Koren,Alisdair R. Fernie,Daniel Zamir,Anthony Bolger,Bjoern Usadel,Bjoern Usadel +19 more
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TLDR
The generation of a comprehensive nanopore sequencing data set with a median read length of 11,979 bp for a self-compatible accession of the wild tomato species Solanum pennellii indicates that such long read sequencing data can be used to affordably sequence and assemble gigabase-sized plant genomes.Abstract:
Updates in nanopore technology have made it possible to obtain gigabases of sequence data. Prior to this, nanopore sequencing technology was mainly used to analyze microbial samples. Here, we describe the generation of a comprehensive nanopore sequencing data set with a median read length of 11,979 bp for a self-compatible accession of the wild tomato species Solanum pennellii. We describe the assembly of its genome to a contig N50 of 2.5 MB. The assembly pipeline comprised initial read correction with Canu and assembly with SMARTdenovo. The resulting raw nanopore-based de novo genome is structurally highly similar to that of the reference S. pennellii LA716 accession but has a high error rate and was rich in homopolymer deletions. After polishing the assembly with Illumina reads, we obtained an error rate of <0.02% when assessed versus the same Illumina data. We obtained a gene completeness of 96.53%, slightly surpassing that of the reference S. pennellii. Taken together, our data indicate that such long read sequencing data can be used to affordably sequence and assemble gigabase-sized plant genomes.read more
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Opportunities and challenges in long-read sequencing data analysis.
Shanika L. Amarasinghe,Shanika L. Amarasinghe,Shian Su,Shian Su,Xueyi Dong,Xueyi Dong,Luke Zappia,Matthew E. Ritchie,Matthew E. Ritchie,Quentin Gouil,Quentin Gouil +10 more
TL;DR: The current landscape of available tools is reviewed, the principles of error correction, base modification detection, and long-read transcriptomics analysis are focused on, and the challenges that remain are highlighted.
Journal ArticleDOI
Overview of Next-Generation Sequencing Technologies.
TL;DR: This review is to provide a compendium of NGS methodologies and associated applications, followed by web links to the manufacturer and/or web‐based visualizations.
Journal ArticleDOI
RaGOO: fast and accurate reference-guided scaffolding of draft genomes
Michael Alonge,Sebastian Soyk,Srividya Ramakrishnan,Xingang Wang,Sara Goodwin,Fritz J. Sedlazeck,Zachary B. Lippman,Zachary B. Lippman,Michael C. Schatz,Michael C. Schatz +9 more
TL;DR: This work presents RaGOO, a reference-guided contig ordering and orienting tool that leverages the speed and sensitivity of Minimap2 to accurately achieve chromosome-scale assemblies in minutes and demonstrates the scalability and utility of the tool.
Journal ArticleDOI
Assessing genome assembly quality using the LTR Assembly Index (LAI).
TL;DR: A reference-free genome metric called LTR Assembly Index (LAI) that evaluates assembly continuity using LTR-RTs is proposed that can facilitate iterative assembly improvement with assembler selection and identify low-quality genomic regions.
Journal ArticleDOI
Chromosome-scale assemblies of plant genomes using nanopore long reads and optical maps
Caroline Belser,Benjamin Istace,Erwan Denis,Marion Dubarry,Franc-Christophe Baurens,Cyril Falentin,Mathieu Genete,Wahiba Berrabah,Anne-Marie Chèvre,Régine Delourme,Gwenaëlle Deniot,Philippe Duffé,Stefan Engelen,Arnaud Lemainque,Maria J. Manzanares-Dauleux,Guillaume Martin,Jérôme Morice,Benjamin Noel,Xavier Vekemans,Angélique D'Hont,Mathieu Rousseau-Gueutin,Valérie Barbe,Corinne Cruaud,Patrick Wincker,Jean-Marc Aury +24 more
TL;DR: A strategy based on long reads (MinION or PromethION sequencers) and optical maps (Saphyr system) that can produce chromosome-level assemblies is described and demonstrated applicability by generating high-quality genome sequences for two new dicotyledon morphotypes.
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