Semi-automated cancer genome analysis using high-performance computing

SAMHD1 is a biomarker for cytarabine response and a therapeutic target in acute myeloid leukemia

(2016) Constanze Schneider et al.   NATURE MEDICINE

Enhanced copy number variants detection from whole-exome sequencing data using EXCAVATOR2

(2016) Romina D'Aurizio et al.   NUCLEIC ACIDS RESEARCH

QuickNGS elevates Next-Generation Sequencing data analysis to a new level of automation

(2015) Prerana Wagle et al.   BMC GENOMICS

Combining tumor genome simulation with crowdsourcing to benchmark somatic single-nucleotide-variant detection

(2015) Adam D Ewing et al.   NATURE METHODS

ExScalibur: A High-Performance Cloud-Enabled Suite for Whole Exome Germline and Somatic Mutation Identification

(2015) Riyue Bao et al.   PLoS One

JAFFA: High sensitivity transcriptome-focused fusion gene detection

(2015) Nadia M Davidson et al.   Genome Medicine

Integrated genomic sequencing reveals mutational landscape of T-cell prolymphocytic leukemia

(2014) M. J. Kiel et al.   BLOOD

TITAN: inference of copy number architectures in clonal cell populations from tumor whole-genome sequence data

(2014) Gavin Ha et al.   GENOME RESEARCH

A general framework for estimating the relative pathogenicity of human genetic variants

(2014) Martin Kircher et al.   NATURE GENETICS

Expanding the computational toolbox for mining cancer genomes

(2014) Li Ding et al.   NATURE REVIEWS GENETICS

BioBlend: automating pipeline analyses within Galaxy and CloudMan

(2013) C. Sloggett et al.   BIOINFORMATICS

Mutational landscape and significance across 12 major cancer types

(2013) Cyriac Kandoth et al.   NATURE

Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples

(2013) Kristian Cibulskis et al.   NATURE BIOTECHNOLOGY

Cancer Genome Landscapes

(2013) B. Vogelstein et al.   SCIENCE

Detecting somatic point mutations in cancer genome sequencing data: a comparison of mutation callers

(2013) Qingguo Wang et al.   Genome Medicine

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Strelka: accurate somatic small-variant calling from sequenced tumor–normal sample pairs

(2012) Christopher T. Saunders et al.   BIOINFORMATICS

A robust model for read count data in exome sequencing experiments and implications for copy number variant calling

(2012) Vincent Plagnol et al.   BIOINFORMATICS

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

(2012) T. Rausch et al.   BIOINFORMATICS

Detecting differential usage of exons from RNA-seq data

(2012) S. Anders et al.   GENOME RESEARCH

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

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

The cBio Cancer Genomics Portal: An Open Platform for Exploring Multidimensional Cancer Genomics Data: Figure 1.

(2012) Ethan Cerami et al.   Cancer Discovery

SomaticSniper: identification of somatic point mutations in whole genome sequencing data

(2011) David E. Larson et al.   BIOINFORMATICS

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

(2011) Mark A DePristo et al.   NATURE GENETICS

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

(2010) A. McKenna et al.   GENOME RESEARCH

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

A method and server for predicting damaging missense mutations

(2010) Ivan A Adzhubei et al.   NATURE METHODS

MutationTaster evaluates disease-causing potential of sequence alterations

(2010) Jana Marie Schwarz et al.   NATURE METHODS

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

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

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm

(2009) Prateek Kumar et al.   Nature Protocols