Evaluating the necessity of PCR duplicate removal from next-generation sequencing data and a comparison of approaches

Next-generation sequencing-based genome diagnostics across clinical genetics centers: implementation choices and their effects

(2015) Terry Vrijenhoek et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

elPrep: High-Performance Preparation of Sequence Alignment/Map Files for Variant Calling

(2015) Charlotte Herzeel et al.   PLoS One

Variant Tool Chest: an improved tool to analyze and manipulate variant call format (VCF) files

(2014) Mark TW Ebbert et al.   BMC BIOINFORMATICS

The rainbow trout genome provides novel insights into evolution after whole-genome duplication in vertebrates

(2014) Camille Berthelot et al.   Nature Communications

ACMG recommendations for reporting of incidental findings in clinical exome and genome sequencing

(2013) Robert C. Green et al.   GENETICS IN MEDICINE

Single nucleotide polymorphism discovery in cutthroat trout subspecies using genome reduction, barcoding, and 454 pyro-sequencing

(2012) Derek D Houston et al.   BMC GENOMICS

An integrated map of genetic variation from 1,092 human genomes

(2012)   NATURE

FastUniq: A Fast De Novo Duplicates Removal Tool for Paired Short Reads

(2012) Haibin Xu et al.   PLoS One

SEAL: a distributed short read mapping and duplicate removal tool

(2011) L. Pireddu et al.   BIOINFORMATICS

The variant call format and VCFtools

(2011) P. Danecek 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

Applications of next-generation sequencing to phylogeography and phylogenetics

(2011) John E. McCormack et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

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

(2011) Mark A DePristo et al.   NATURE GENETICS

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

(2010) Heng Li et al.   BIOINFORMATICS

A map of human genome variation from population-scale sequencing

(2010) Richard M. Durbin et al.   NATURE

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

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

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Next-Generation Sequencing: From Basic Research to Diagnostics

(2009) K. V. Voelkerding et al.   CLINICAL CHEMISTRY

Profiling the HeLa S3 transcriptome using randomly primed cDNA and massively parallel short-read sequencing

(2008) Ryan D. Morin et al.   BIOTECHNIQUES