Detrimental effects of duplicate reads and low complexity regions on RNA- and ChIP-seq data

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Reconstructing complex regions of genomes using long-read sequencing technology

(2014) J. Huddleston et al.   GENOME RESEARCH

Detection of Structural Variants Involving Repetitive Regions in the Reference Genome

(2014) Heewook Lee et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Detection of Gene Rearrangements in Targeted Clinical Next-Generation Sequencing

(2014) Haley J. Abel et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

An Extensive Evaluation of Read Trimming Effects on Illumina NGS Data Analysis

(2013) Cristian Del Fabbro et al.   PLoS One

Pervasive Transcription of the Human Genome Produces Thousands of Previously Unidentified Long Intergenic Noncoding RNAs

(2013) Matthew J. Hangauer et al.   PLoS Genetics

An integrated map of genetic variation from 1,092 human genomes

(2012)   NATURE

Systematic evaluation of factors influencing ChIP-seq fidelity

(2012) Yiwen Chen et al.   NATURE METHODS

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

ChIP–seq and beyond: new and improved methodologies to detect and characterize protein–DNA interactions

(2012) Terrence S. Furey   NATURE REVIEWS GENETICS

ENCODE Data in the UCSC Genome Browser: year 5 update

(2012) Kate R. Rosenbloom et al.   NUCLEIC ACIDS RESEARCH

False positive peaks in ChIP-seq and other sequencing-based functional assays caused by unannotated high copy number regions

(2011) Joseph K. Pickrell et al.   BIOINFORMATICS

MEME-ChIP: motif analysis of large DNA datasets

(2011) Philip Machanick et al.   BIOINFORMATICS

Quality control and preprocessing of metagenomic datasets

(2011) R. Schmieder et al.   BIOINFORMATICS

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

Discovering Transcription Factor Binding Sites in Highly Repetitive Regions of Genomes with Multi-Read Analysis of ChIP-Seq Data

(2011) Dongjun Chung et al.   PLoS Computational Biology

RNA-Seq gene expression estimation with read mapping uncertainty

(2009) Bo Li et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Increased PDGFRα Activation Disrupts Connective Tissue Development and Drives Systemic Fibrosis

(2009) Lorin E. Olson et al.   DEVELOPMENTAL CELL

Computational methods for discovering structural variation with next-generation sequencing

(2009) Paul Medvedev et al.   NATURE METHODS

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

A universal classification of eukaryotic transposable elements implemented in Repbase

(2008) Vladimir V. Kapitonov et al.   NATURE REVIEWS GENETICS