systemPipeR: NGS workflow and report generation environment

RAP: RNA-Seq Analysis Pipeline, a new cloud-based NGS web application

(2015) Mattia D'Antonio et al.   BMC GENOMICS

BatchJobsandBatchExperiments: Abstraction Mechanisms for UsingRin Batch Environments

(2015) Bernd Bischl et al.   Journal of Statistical Software

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

Orchestrating high-throughput genomic analysis with Bioconductor

(2015) Wolfgang Huber et al.   NATURE METHODS

VariantAnnotation: a Bioconductor package for exploration and annotation of genetic variants

(2014) V. Obenchain et al.   BIOINFORMATICS

QuasR: quantification and annotation of short reads in R

(2014) Dimos Gaidatzis et al.   BIOINFORMATICS

Launching genomics into the cloud: deployment of Mercury, a next generation sequence analysis pipeline

(2014) Jeffrey G Reid et al.   BMC BIOINFORMATICS

The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells

(2014) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

BioBlend: automating pipeline analyses within Galaxy and CloudMan

(2013) C. Sloggett et al.   BIOINFORMATICS

The Taverna workflow suite: designing and executing workflows of Web Services on the desktop, web or in the cloud

(2013) Katherine Wolstencroft et al.   NUCLEIC ACIDS RESEARCH

Use of Whole Genome Sequencing to Determine the Microevolution of Mycobacterium tuberculosis during an Outbreak

(2013) Midori Kato-Maeda et al.   PLoS One

Software for Computing and Annotating Genomic Ranges

(2013) Michael Lawrence et al.   PLoS Computational Biology

Snakemake--a scalable bioinformatics workflow engine

(2012) J. Koster et al.   BIOINFORMATICS

Workflows for microarray data processing in the Kepler environment

(2012) Thomas Stropp et al.   BMC BIOINFORMATICS

The Wasp System: An open source environment for managing and analyzing genomic data

(2012) Andrew S. McLellan et al.   GENOMICS

Scientific workflow systems: Pipeline Pilot and KNIME

(2012) Wendy A. Warr   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles

(2012) Altuna Akalin et al.   GENOME BIOLOGY

Next Generation Sequence Analysis and Computational Genomics Using Graphical Pipeline Workflows

(2012) Federica Torri et al.   Genes

A high-resolution map of human evolutionary constraint using 29 mammals

(2011) Kerstin Lindblad-Toh et al.   NATURE

Harnessing cloud computing with Galaxy Cloud

(2011) Enis Afgan et al.   NATURE BIOTECHNOLOGY

Single-cell genomics

(2011) Tomer Kalisky et al.   NATURE METHODS

Ruffus: a lightweight Python library for computational pipelines

(2010) Leo Goodstadt   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

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

(2010) A. McKenna et al.   GENOME RESEARCH

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

(2010) Jeremy Goecks et al.   GENOME BIOLOGY

ShortRead: a bioconductor package for input, quality assessment and exploration of high-throughput sequence data

(2009) M. Morgan et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(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

The new paradigm of flow cell sequencing

(2008) R. A. Holt et al.   GENOME RESEARCH

Design and analysis of ChIP-seq experiments for DNA-binding proteins

(2008) Peter V Kharchenko et al.   NATURE BIOTECHNOLOGY

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY