VDAP-GUI: a user-friendly pipeline for variant discovery and annotation of raw next-generation sequencing data

Whole-exome sequencing of pancreatic cancer defines genetic diversity and therapeutic targets

(2015) Agnieszka K. Witkiewicz et al.   Nature Communications

WEP: a high-performance analysis pipeline for whole-exome data

(2013) Mattia D'Antonio et al.   BMC BIOINFORMATICS

Atlas2 Cloud: a framework for personal genome analysis in the cloud

(2012) Uday S Evani et al.   BMC GENOMICS

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

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

(2011) Xutao Deng   BMC BIOINFORMATICS

ngs_backbone: a pipeline for read cleaning, mapping and SNP calling using Next Generation Sequence

(2011) Jose M Blanca et al.   BMC GENOMICS

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

(2011) Mark A DePristo et al.   NATURE GENETICS

Computational and statistical approaches to analyzing variants identified by exome sequencing

(2011) Nathan O Stitziel et al.   GENOME BIOLOGY

GAMES identifies and annotates mutations in next-generation sequencing projects

(2010) M. E. Sana et al.   BIOINFORMATICS

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

(2010) Heng Li et al.   BIOINFORMATICS

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data

(2010) K. Wang et al.   NUCLEIC ACIDS RESEARCH

VarScan: variant detection in massively parallel sequencing of individual and pooled samples

(2009) Daniel C. Koboldt et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Sequencing technologies — the next generation

(2009) Michael L. Metzker   NATURE REVIEWS GENETICS

Next-generation DNA sequencing

(2008) Jay Shendure et al.   NATURE BIOTECHNOLOGY