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

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

(2013) Daehwan Kim et al.   GENOME BIOLOGY

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

Activating Transcription Factor 3 Regulates Immune and Metabolic Homeostasis

(2012) J. Rynes et al.   MOLECULAR AND CELLULAR BIOLOGY

Identifying ChIP-seq enrichment using MACS

(2012) Jianxing Feng et al.   Nature Protocols

Using Drosophila melanogaster as a Model for Genotoxic Chemical Mutational Studies with a New Program, SnpSift

(2012) Pablo Cingolani et al.   Frontiers in Genetics

MEME-ChIP: motif analysis of large DNA datasets

(2011) Philip Machanick et al.   BIOINFORMATICS

Chipster: user-friendly analysis software for microarray and other high-throughput data

(2011) M Aleksi Kallio et al.   BMC GENOMICS

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

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

Discovering microRNAs from deep sequencing data using miRDeep

(2008) Marc R Friedländer et al.   NATURE BIOTECHNOLOGY