RUbioSeq: a suite of parallelized pipelines to automate exome variation and bisulfite-seq analyses

CONTRA: copy number analysis for targeted resequencing

(2012) Jason Li et al.   BIOINFORMATICS

Detecting and annotating genetic variations using the HugeSeq pipeline

(2012) Hugo Y K Lam et al.   NATURE BIOTECHNOLOGY

DNA methylome analysis using short bisulfite sequencing data

(2012) Felix Krueger et al.   NATURE METHODS

New Mutations in Chronic Lymphocytic Leukemia Identified by Target Enrichment and Deep Sequencing

(2012) Elena Doménech et al.   PLoS One

NARWHAL, a primary analysis pipeline for NGS data

(2011) R. W. W. Brouwer et al.   BIOINFORMATICS

The variant call format and VCFtools

(2011) P. Danecek 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 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

Human DNA methylomes at base resolution show widespread epigenomic differences

(2009) Ryan Lister et al.   NATURE

BFAST: An Alignment Tool for Large Scale Genome Resequencing

(2009) Nils Homer et al.   PLoS One

Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning

(2008) Shawn J. Cokus et al.   NATURE