GenPipes: an open-source framework for distributed and scalable genomic analyses

GenPipes: an open-source framework for distributed and scalable genomic analyses

(2019) Mathieu Bourgey et al.   GigaScience

SvABA: genome-wide detection of structural variants and indels by local assembly

(2018) Jeremiah A. Wala et al.   GENOME RESEARCH

Global characterization of copy number variants in epilepsy patients from whole genome sequencing

(2018) Jean Monlong et al.   PLoS Genetics

Nextflow enables reproducible computational workflows

(2017) Paolo Di Tommaso et al.   NATURE BIOTECHNOLOGY

Contribution to Alzheimer's disease risk of rare variants in TREM2, SORL1, and ABCA7 in 1779 cases and 1273 controls

(2017) Céline Bellenguez et al.   NEUROBIOLOGY OF AGING

Kronos: a workflow assembler for genome analytics and informatics

(2017) M. Jafar Taghiyar et al.   GigaScience

Identification of Elongated Primary Cilia with Impaired Mechanotransduction in Idiopathic Scoliosis Patients

(2017) Niaz Oliazadeh et al.   Scientific Reports

MultiQC: summarize analysis results for multiple tools and samples in a single report

(2016) Philip Ewels et al.   BIOINFORMATICS

Integrated (epi)-Genomic Analyses Identify Subgroup-Specific Therapeutic Targets in CNS Rhabdoid Tumors

(2016) Jonathon Torchia et al.   CANCER CELL

The International Human Epigenome Consortium: A Blueprint for Scientific Collaboration and Discovery

(2016) Hendrik G. Stunnenberg et al.   CELL

dbNSFP v3.0: A One-Stop Database of Functional Predictions and Annotations for Human Nonsynonymous and Splice-Site SNVs

(2016) Xiaoming Liu et al.   HUMAN MUTATION

17q21.31 duplication causes prominent tau-related dementia with increased MAPT expression

(2016) K Le Guennec et al.   MOLECULAR PSYCHIATRY

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

VarDict: a novel and versatile variant caller for next-generation sequencing in cancer research

(2016) Zhongwu Lai et al.   NUCLEIC ACIDS RESEARCH

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update

(2016) Enis Afgan et al.   NUCLEIC ACIDS RESEARCH

ERRα mediates metabolic adaptations driving lapatinib resistance in breast cancer

(2016) Geneviève Deblois et al.   Nature Communications

eFORGE: A Tool for Identifying Cell Type-Specific Signal in Epigenomic Data

(2016) Charles E. Breeze et al.   Cell Reports

CNVkit: Genome-Wide Copy Number Detection and Visualization from Targeted DNA Sequencing

(2016) Eric Talevich et al.   PLoS Computational Biology

VSEARCH: a versatile open source tool for metagenomics

(2016) Torbjørn Rognes et al.   PeerJ

Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments

(2016) Neva C. Durand et al.   Cell Systems

Extensive sequencing of seven human genomes to characterize benchmark reference materials

(2016) Justin M. Zook et al.   Scientific Data

Omics Pipe: a community-based framework for reproducible multi-omics data analysis

(2015) Kathleen M. Fisch et al.   BIOINFORMATICS

MetaSV: an accurate and integrative structural-variant caller for next generation sequencing

(2015) Marghoob Mohiyuddin et al.   BIOINFORMATICS

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

(2015) Adam D Ewing et al.   NATURE METHODS

TopDom: an efficient and deterministic method for identifying topological domains in genomes

(2015) Hanjun Shin et al.   NUCLEIC ACIDS RESEARCH

Wham: Identifying Structural Variants of Biological Consequence

(2015) Zev N. Kronenberg et al.   PLoS Computational Biology

Genome Modeling System: A Knowledge Management Platform for Genomics

(2015) Malachi Griffith et al.   PLoS Computational Biology

Changes in the expression profiles of claudins during gonocyte differentiation and in seminomas

(2015) G. Manku et al.   Andrology

NGSANE: a lightweight production informatics framework for high-throughput data analysis

(2014) Fabian A. Buske et al.   BIOINFORMATICS

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

BigDataScript: a scripting language for data pipelines

(2014) P. Cingolani et al.   BIOINFORMATICS

Genomic analysis of diffuse intrinsic pontine gliomas identifies three molecular subgroups and recurrent activating ACVR1 mutations

(2014) Pawel Buczkowicz et al.   NATURE GENETICS

Variation in genomic landscape of clear cell renal cell carcinoma across Europe

(2014) Ghislaine Scelo et al.   Nature Communications

LUMPY: a probabilistic framework for structural variant discovery

(2014) Ryan M Layer et al.   GENOME BIOLOGY

Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data

(2013) Chen-Shan Chin et al.   NATURE METHODS

GEMINI: Integrative Exploration of Genetic Variation and Genome Annotations

(2013) Umadevi Paila et al.   PLoS Computational Biology

Bpipe: a tool for running and managing bioinformatics pipelines

(2012) Simon P. Sadedin et al.   BIOINFORMATICS

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

(2012) T. Rausch et al.   BIOINFORMATICS

RNA-SeQC: RNA-seq metrics for quality control and process optimization

(2012) David S. DeLuca et al.   BIOINFORMATICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Snakemake--a scalable bioinformatics workflow engine

(2012) J. Koster et al.   BIOINFORMATICS

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

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

Differential analysis of gene regulation at transcript resolution with RNA-seq

(2012) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Bis-SNP: Combined DNA methylation and SNP calling for Bisulfite-seq data

(2012) Yaping Liu et al.   GENOME BIOLOGY

Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications

(2011) Felix Krueger et al.   BIOINFORMATICS

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

FLASH: fast length adjustment of short reads to improve genome assemblies

(2011) T. Magoc et al.   BIOINFORMATICS

SeqWare Query Engine: storing and searching sequence data in the cloud

(2011) Brian D O’Connor et al.   BMC BIOINFORMATICS

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

The $1,000 genome, the $100,000 analysis?

(2010) Elaine R Mardis   Genome Medicine

Gene ontology analysis for RNA-seq: accounting for selection bias

(2010) Matthew D Young et al.   GENOME BIOLOGY

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

PyNAST: a flexible tool for aligning sequences to a template alignment

(2009) J. G. Caporaso et al.   BIOINFORMATICS

FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix

(2009) M. N. Price et al.   MOLECULAR BIOLOGY AND EVOLUTION

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY