Journal ArticleDOI
Third generation sequencing: technology and its potential impact on evolutionary biodiversity research
TLDR
The recent technical advancements of third generation sequencing instruments are reviewed, thereby covering nanopore sequencing and single molecule real-time (SMRT) sequencing.Abstract:
Next generation sequencing transformed the field of evolutionary biology and high throughput sequencing platforms are routinely used in phylogenomic, population genomic or metagenomic studies. Here I review the recent technical advancements of third generation sequencing instruments, thereby covering nanopore sequencing and single molecule real-time (SMRT) sequencing. The output and error rates are compared with sequencing platforms of the second generation (454 pyrosequencing, Illumina and Ion Torrent). Third generation sequencers produce sequence reads in hitherto unprecedented lengths and will help to strongly increase the quality of genome assemblies. Moreover, the speed of sequencing and ease of sample preparation enables sequencing in the field. Even though the output and error rate of the new generation of sequencer remains to be improved, new possibilities for evolutionary research will open up in the near future by these new techniques.read more
Citations
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Journal ArticleDOI
DnaSP 6: DNA Sequence Polymorphism Analysis of Large Data Sets.
Julio Rozas,Albert Ferrer-Mata,Juan Carlos Sánchez-DelBarrio,Sara Guirao-Rico,Pablo Librado,Pablo Librado,Sebastian E. Ramos-Onsins,Alejandro Sánchez-Gracia +7 more
TL;DR: The DNA Sequence Polymorphism (DnaSP) software as mentioned in this paper is a popular tool for performing exhaustive population genetic analyses on multiple sequence alignments, such as single and multi-locus coalescent simulations under a wide range of demographic scenarios.
Journal ArticleDOI
PacBio metabarcoding of Fungi and other eukaryotes: errors, biases and perspectives.
TL;DR: It is concluded that PacBio sequencing provides a viable alternative for metabarcoding of organisms that are of relatively low diversity, require > 500-bp barcode for reliable identification or when phylogenetic approaches are intended.
Journal ArticleDOI
Whole-genome sequencing approaches for conservation biology: Advantages, limitations and practical recommendations
TL;DR: No single WGR approach fulfils all requirements of conservation genetics, and each method has its own limitations and sources of potential bias; proposed ways to minimize such biases are discussed.
Journal ArticleDOI
Detection of Plant Viruses and Disease Management: Relevance of Genetic Diversity and Evolution.
TL;DR: The techniques used for plant virus diagnosis and disease control are reviewed, including characteristics such as accuracy, detection level, multiplexing, quantification, portability, and designability.
References
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Journal ArticleDOI
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Journal ArticleDOI
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Journal ArticleDOI
Accurate whole human genome sequencing using reversible terminator chemistry
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TL;DR: An approach that generates several billion bases of accurate nucleotide sequence per experiment at low cost is reported, effective for accurate, rapid and economical whole-genome re-sequencing and many other biomedical applications.
Journal ArticleDOI
Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data
Chen-Shan Chin,David Alexander,Patrick Marks,Aaron Klammer,James P Drake,Cheryl Heiner,Alicia Clum,Alex Copeland,John Huddleston,Evan E. Eichler,Stephen Turner,Jonas Korlach +11 more
TL;DR: This work presents a hierarchical genome-assembly process (HGAP) for high-quality de novo microbial genome assemblies using only a single, long-insert shotgun DNA library in conjunction with Single Molecule, Real-Time (SMRT) DNA sequencing.