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Journal ArticleDOI

Next-Generation DNA Sequencing Methods

TLDR
An astounding potential exists for next-generation DNA sequencing technologies to bring enormous change in genetic and biological research and to enhance the authors' fundamental biological knowledge.
Abstract
Recent scientific discoveries that resulted from the application of nextgeneration DNA sequencing technologies highlight the striking impact of these massively parallel platforms on genetics. These new methods have expanded previously focused readouts from a variety of DNA preparation protocols to a genome-wide scale and have fine-tuned their resolution to single base precision. The sequencing of RNA also has transitioned and now includes full-length cDNA analyses, serial analysis of gene expression (SAGE)-based methods, and noncoding RNA discovery. Next-generation sequencing has also enabled novel applications such as the sequencing of ancient DNA samples, and has substantially widened the scope of metagenomic analysis of environmentally derived samples. Taken together, an astounding potential exists for these technologies to bring enormous change in genetic and biological research and to enhance our fundamental biological knowledge.

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Citations
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Journal ArticleDOI

The Sequence Alignment/Map format and SAMtools

TL;DR: SAMtools as discussed by the authors implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments.
Journal ArticleDOI

Trimmomatic: a flexible trimmer for Illumina sequence data

TL;DR: Timmomatic is developed as a more flexible and efficient preprocessing tool, which could correctly handle paired-end data and is shown to produce output that is at least competitive with, and in many cases superior to, that produced by other tools, in all scenarios tested.
Journal ArticleDOI

NGS QC Toolkit: a toolkit for quality control of next generation sequencing data.

Ravi K. Patel, +1 more
- 01 Feb 2012 - 
TL;DR: The toolkit is comprised of user-friendly tools for QC of sequencing data generated using Roche 454 and Illumina platforms, and additional tools to aid QC (sequence format converter and trimming tools) and analysis and analysis (statistics tools).
Journal ArticleDOI

Rare-Variant Association Testing for Sequencing Data with the Sequence Kernel Association Test

TL;DR: The sequence kernel association test (SKAT) is proposed, a supervised, flexible, computationally efficient regression method to test for association between genetic variants (common and rare) in a region and a continuous or dichotomous trait while easily adjusting for covariates.
References
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Journal ArticleDOI

Initial sequencing and analysis of the human genome.

Eric S. Lander, +248 more
- 15 Feb 2001 - 
TL;DR: The results of an international collaboration to produce and make freely available a draft sequence of the human genome are reported and an initial analysis is presented, describing some of the insights that can be gleaned from the sequence.
Journal ArticleDOI

The sequence of the human genome.

J. Craig Venter, +272 more
- 16 Feb 2001 - 
TL;DR: Comparative genomic analysis indicates vertebrate expansions of genes associated with neuronal function, with tissue-specific developmental regulation, and with the hemostasis and immune systems are indicated.
Journal ArticleDOI

An obesity-associated gut microbiome with increased capacity for energy harvest

TL;DR: It is demonstrated through metagenomic and biochemical analyses that changes in the relative abundance of the Bacteroidetes and Firmicutes affect the metabolic potential of the mouse gut microbiota and indicates that the obese microbiome has an increased capacity to harvest energy from the diet.
Journal ArticleDOI

Obesity alters gut microbial ecology

TL;DR: Analysis of the microbiota of genetically obese ob/ob mice, lean ob/+ and wild-type siblings, and their ob/+ mothers, all fed the same polysaccharide-rich diet, indicates that obesity affects the diversity of the gut microbiota and suggests that intentional manipulation of community structure may be useful for regulating energy balance in obese individuals.
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