From Wet-Lab to Variations: Concordance and Speed of Bioinformatics Pipelines for Whole Genome and Whole Exome Sequencing

Medical implications of technical accuracy in genome sequencing

(2016) Rachel L. Goldfeder et al.   Genome Medicine

Utility of whole-exome sequencing for those near the end of the diagnostic odyssey: time to address gaps in care

(2015) S.L. Sawyer et al.   CLINICAL GENETICS

Genetic diagnosis of developmental disorders in the DDD study: a scalable analysis of genome-wide research data

(2015) Caroline F Wright et al.   LANCET

Leveraging the Power of High Performance Computing for Next Generation Sequencing Data Analysis: Tricks and Twists from a High Throughput Exome Workflow

(2015) Amit Kawalia et al.   PLoS One

An analytical framework for optimizing variant discovery from personal genomes

(2015) Gareth Highnam et al.   Nature Communications

A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing

(2015) Tyler S. Alioto et al.   Nature Communications

Achieving high-sensitivity for clinical applications using augmented exome sequencing

(2015) Anil Patwardhan et al.   Genome Medicine

A Comparison of Variant Calling Pipelines Using Genome in a Bottle as a Reference

(2015) Adam Cornish et al.   Biomed Research International

Churchill: an ultra-fast, deterministic, highly scalable and balanced parallelization strategy for the discovery of human genetic variation in clinical and population-scale genomics

(2015) Benjamin J Kelly et al.   GENOME BIOLOGY

Systematic comparison of variant calling pipelines using gold standard personal exome variants

(2015) Sohyun Hwang et al.   Scientific Reports

Molecular Findings Among Patients Referred for Clinical Whole-Exome Sequencing

(2014) Yaping Yang et al.   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

Clinical Interpretation and Implications of Whole-Genome Sequencing

(2014) Frederick E. Dewey et al.   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

Integrating human sequence data sets provides a resource of benchmark SNP and indel genotype calls

(2014) Justin M Zook et al.   NATURE BIOTECHNOLOGY

Diagnostic Clinical Genome and Exome Sequencing

(2014) Leslie G. Biesecker et al.   NEW ENGLAND JOURNAL OF MEDICINE

Reducing INDEL calling errors in whole genome and exome sequencing data

(2014) Han Fang et al.   Genome Medicine

Detailed comparison of two popular variant calling packages for exome and targeted exon studies

(2014) Charles D. Warden et al.   PeerJ

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

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

DELLY: structural variant discovery by integrated paired-end and split-read analysis

(2012) T. Rausch et al.   BIOINFORMATICS

The GEM mapper: fast, accurate and versatile alignment by filtration

(2012) Santiago Marco-Sola et al.   NATURE METHODS

Fast Computation and Applications of Genome Mappability

(2012) Thomas Derrien et al.   PLoS One

Control-FREEC: a tool for assessing copy number and allelic content using next-generation sequencing data

(2011) Valentina Boeva et al.   BIOINFORMATICS

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

(2011) H. Li   BIOINFORMATICS

VennDiagram: a package for the generation of highly-customizable Venn and Euler diagrams in R

(2011) Hanbo Chen et al.   BMC BIOINFORMATICS

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

(2011) Mark A DePristo et al.   NATURE GENETICS