Broad Institute

The Sequence Alignment/Map format and SAMtools

Abstract Summary: The Sequence Alignment/Map (SAM) format is a generic alignment format for storing read alignments against reference sequences, supporting short and long reads ...

Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles

Although genomewide RNA expression analysis has become a routine tool in biomedical research, extracting biological insight from such information remains a major challenge. Here...

PLINK: A Tool Set for Whole-Genome Association and Population-Based Linkage Analyses

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

Next-generation DNA sequencing (NGS) projects, such as the 1000 Genomes Project, are already revolutionizing our understanding of genetic variation among individuals. However, t...

Full-length transcriptome assembly from RNA-Seq data without a reference genome

A global reference for human genetic variation

Model-based Analysis of ChIP-Seq (MACS)

The variant call format and VCFtools

Abstract Summary: The variant call format (VCF) is a generic format for storing DNA polymorphism data such as SNPs, insertions, deletions and structural variants, together with ...

Integrative genomics viewer

UCHIME improves sensitivity and speed of chimera detection

Abstract Motivation: Chimeric DNA sequences often form during polymerase chain reaction amplification, especially when sequencing single regions (e.g. 16S rRNA or fungal Interna...