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Software

Scientists in the Broad community have developed many critical software tools for the analysis of increasingly large genome-related datasets, and they make these tools openly available to the scientific community. For the conditions governing the use of Broad Institute software, please see the software use agreement associated with the tools you choose to download.

Use our search function, browse the complete software collection or click on one of the software categories listed below:

All   Chemical Biology     Image Analysis     Proteomics     Portals     Tool Suites    Visualization
Genetic Analysis:   GWAS   Genetic Variation   Linkage Analysis   Gene Expression
Sequence Analysis:   Assembly   Annotation   Alignment   RNAi   RNA-seq   Primer Design   Next Generation Tools   Phylogenetic Analysis   Gene Structure  Viral

  • ALLPATHS

    ALLPATHS is a whole genome shotgun assembler that can generate high quality assemblies from short reads.

  • AmosCmp16Spipeline

    AmosCmp16Spipeline uses the AMOScmp software to assemble multiple, potentially overlapping 16S rRNA sequencing reads based on read mappings to a reference 16S rRNA gene.

  • Arachne

    Arachne is a tool for assembling genome sequences from whole genome shotgun reads, mostly in forward-reverse pairs obtained by sequencing clone ends.

  • Argo

    The Argo Genome Browser is a production tool for visualizing and manually annotating whole genomes.

  • AV454

    AssembleViral454 is a new assembler, based on the ARACHNE package, designed for small and non-repetitive genomes sequenced at high depth. It was specifically designed to assemble read data generated from a mixed population of viral genomes. Reads need not be paired, and it is assumed that no sequence repeat in the genome would be large enough to fully contain an average read. The assembly process consists of two steps: First, a pre-processing stage is run, the output of which is an initial read layout. This is identical to the process employed in the published ARACHNE algorithm. This stage generally results in a fragmented assembly. Second, we employ an iterative procedure that incrementally merges contigs and improves read placement.

  • Birdsuite

    The Birdsuite is a fully open-source set of tools to detect and report SNP genotypes, common Copy-Number Polymorphisms (CNPs), and novel, rare, or de novo CNVs in samples processed with the Affymetrix platform.

  • Broad-Novartis Cancer Cell Line Encyclopedia (CCLE)

    The Cancer Cell Line Encyclopedia (CCLE) project is a collaboration between the Broad Institute, and the Novartis Institutes for Biomedical Research and its Genomics Institute of the Novartis Research Foundation to conduct a detailed genetic and pharmacologic characterization of a large panel of human cancer models, to develop integrated computational analyses that link distinct pharmacologic vulnerabilities to genomic patterns and to translate cell line integrative genomics into cancer patient stratification. The CCLE provides public access analysis and visualization of DNA copy number, mRNA expression and mutation data for about 1000 cell lines. 

  • Butterfly

    Butterfly then processes the individual graphs in parallel, tracing the paths that reads and pairs of reads take within the graph, ultimately reporting full-length transcripts for alternatively spliced isoforms, and teasing apart transcripts that corresponds to paralogous genes.

  • Cancer Portals

    A number of cancer portals have been developed to streamline viewing and analysis of related data.

  • CellProfiler

    CellProfiler cell image analysis software quantitatively measures phenotypes from thousands of images automatically, usually for high-throughput image-based cell screening experiments.