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PyroHMMsnp: an SNP caller for Ion Torrent and 454 sequencing data

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Low concordance of multiple variant-calling pipelines: practical implications for exome and genome sequencing

(2013) Jason O'Rawe et al.   Genome Medicine

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Pacific biosciences sequencing technology for genotyping and variation discovery in human data

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Next-generation sequencing: ready for the clinics?

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VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing

(2012) D. C. Koboldt et al.   GENOME RESEARCH

A beginners guide to SNP calling from high-throughput DNA-sequencing data

(2012) André Altmann et al.   HUMAN GENETICS

Sequence analysis of mutations and translocations across breast cancer subtypes

(2012) Shantanu Banerji et al.   NATURE

Exome sequencing identifies recurrent SPOP, FOXA1 and MED12 mutations in prostate cancer

(2012) Christopher E Barbieri et al.   NATURE GENETICS

Exome sequencing of gastric adenocarcinoma identifies recurrent somatic mutations in cell adhesion and chromatin remodeling genes

(2012) Zhi Jiang Zang et al.   NATURE GENETICS

Evolution and Functional Impact of Rare Coding Variation from Deep Sequencing of Human Exomes

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SeqGene: a comprehensive software solution for mining exome- and transcriptome- sequencing data

(2011) Xutao Deng   BMC BIOINFORMATICS

Performance comparison of whole-genome sequencing platforms

(2011) Hugo Y K Lam et al.   NATURE BIOTECHNOLOGY

Performance comparison of exome DNA sequencing technologies

(2011) Michael J Clark et al.   NATURE BIOTECHNOLOGY

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

Needles in stacks of needles: finding disease-causal variants in a wealth of genomic data

(2011) Gregory M. Cooper et al.   NATURE REVIEWS GENETICS

Exome sequencing as a tool for Mendelian disease gene discovery

(2011) Michael J. Bamshad et al.   NATURE REVIEWS GENETICS

Genotype and SNP calling from next-generation sequencing data

(2011) Rasmus Nielsen et al.   NATURE REVIEWS GENETICS

The functional spectrum of low-frequency coding variation

(2011) Gabor T Marth et al.   GENOME BIOLOGY

Unlocking Mendelian disease using exome sequencing

(2011) Christian Gilissen et al.   GENOME BIOLOGY

Computational and statistical approaches to analyzing variants identified by exome sequencing

(2011) Nathan O Stitziel et al.   GENOME BIOLOGY

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

A survey of sequence alignment algorithms for next-generation sequencing

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Making a definitive diagnosis: Successful clinical application of whole exome sequencing in a child with intractable inflammatory bowel disease

(2010) Elizabeth A Worthey et al.   GENETICS IN MEDICINE

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

A map of human genome variation from population-scale sequencing

(2010) Richard M. Durbin et al.   NATURE

Advances in understanding cancer genomes through second-generation sequencing

(2010) Matthew Meyerson et al.   NATURE REVIEWS GENETICS

Uncovering the roles of rare variants in common disease through whole-genome sequencing

(2010) Elizabeth T. Cirulli et al.   NATURE REVIEWS GENETICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

SNP detection for massively parallel whole-genome resequencing

(2009) R. Li et al.   GENOME RESEARCH

Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing

(2009) Andreas Gnirke et al.   NATURE BIOTECHNOLOGY

Sequencing technologies — the next generation

(2009) Michael L. Metzker   NATURE REVIEWS GENETICS

Potential etiologic and functional implications of genome-wide association loci for human diseases and traits

(2009) L. A. Hindorff et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mapping short DNA sequencing reads and calling variants using mapping quality scores

(2008) H. Li et al.   GENOME RESEARCH

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(2008) Jay Shendure et al.   NATURE BIOTECHNOLOGY

Pyrobayes: an improved base caller for SNP discovery in pyrosequences

(2008) Aaron R Quinlan et al.   NATURE METHODS