Simulating Next-Generation Sequencing Datasets from Empirical Mutation and Sequencing Models

Non-coding recurrent mutations in chronic lymphocytic leukaemia

(2015) Xose S. Puente et al.   NATURE

A global reference for human genetic variation

(2015) Richard A. Gibbs et al.   NATURE

VarSim: a high-fidelity simulation and validation framework for high-throughput genome sequencing with cancer applications

(2014) John C. Mu et al.   BIOINFORMATICS

SInC: an accurate and fast error-model based simulator for SNPs, Indels and CNVs coupled with a read generator for short-read sequence data

(2014) Swetansu Pattnaik et al.   BMC BIOINFORMATICS

Comparison of mapping algorithms used in high-throughput sequencing: application to Ion Torrent data

(2014) Ségolène Caboche et al.   BMC GENOMICS

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

(2014) Justin M Zook et al.   NATURE BIOTECHNOLOGY

Reduced local mutation density in regulatory DNA of cancer genomes is linked to DNA repair

(2013) Paz Polak et al.   NATURE BIOTECHNOLOGY

pIRS: Profile-based Illumina pair-end reads simulator

(2012) Xuesong Hu et al.   BIOINFORMATICS

GemSIM: general, error-model based simulator of next-generation sequencing data

(2012) Kerensa E McElroy et al.   BMC GENOMICS

A Landscape of Driver Mutations in Melanoma

(2012) Eran Hodis et al.   CELL

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

ART: a next-generation sequencing read simulator

(2011) Weichun Huang et al.   BIOINFORMATICS

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

The NumPy Array: A Structure for Efficient Numerical Computation

(2011) Stéfan van der Walt et al.   COMPUTING IN SCIENCE & ENGINEERING

Variation in the mutation rate across mammalian genomes

(2011) Alan Hodgkinson et al.   NATURE REVIEWS GENETICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

TP53 Mutations in Human Cancers: Origins, Consequences, and Clinical Use

(2009) M. Olivier et al.   Cold Spring Harbor Perspectives in Biology

Are animal models predictive for humans?

(2009) Niall Shanks et al.   Philosophy Ethics and Humanities in Medicine

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

(2008) H. Li et al.   GENOME RESEARCH