I-ATAC: interactive pipeline for the management and pre-processing of ATAC-seq samples

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

SMITH: a LIMS for handling next-generation sequencing workflows

(2014) Francesco Venco et al.   BMC BIOINFORMATICS

Chromatin accessibility: a window into the genome

(2014) Maria Tsompana et al.   Epigenetics & Chromatin

Galaxy LIMS for next-generation sequencing

(2013) J. Scholtalbers et al.   BIOINFORMATICS

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

(2013) Jason D Buenrostro et al.   NATURE METHODS

NG6: Integrated next generation sequencing storage and processing environment

(2012) Jérôme Mariette et al.   BMC GENOMICS

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

(2012) Andrew S. McLellan et al.   GENOMICS

openBIS: a flexible framework for managing and analyzing complex data in biology research

(2011) Angela Bauch et al.   BMC BIOINFORMATICS

Ergatis: a web interface and scalable software system for bioinformatics workflows

(2010) J. Orvis et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

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

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY