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:

  • Pilon

    Pilon uses read alignment analysis to diagnose, report, and automatically improve genome assemblies, and it can also be used to make variant calls among similar haploid strains.


    PLINK is a comprehensive toolset for statistical analysis in whole-genome association studies.

  • Primer3

    Primer3 is a tool used to choose primers for PCR reactions.

  • PriSM

    PriSM is a set of algorithms designed specifically to create degenerate primers for the amplification and sequencing of short viral genomes while maintaining sample population diversity.

  • Project Achilles Data Portal

    Project Achilles is a systematic effort aimed at identifying and cataloging genetic vulnerabilities across hundreds of genomically characterized cancer cell lines. The project uses a genome-wide shRNA library to silence individual genes and identify those genes that affect cell survival. Large-scale functional screening of cancer cell lines provides a complementary approach to those studies that aim to characterize the molecular alterations (mutations, copy number alterations, etc.) of primary tumors, such as The Cancer Genome Atlas. The overall goal of the project is to link cancer genetic dependencies to their molecular characteristics in order to Identify molecular targets and guide therapeutic development.

  • RC454

    RC454 is a program that takes a set of 454 read and quality files as well as a consensus assembly for those reads and corrects for known 454 error modes such as homopolymer indels and carry forward/incomplete extension (CAFIE). It will also correct for any indel that breaks the reading frame, unless it occurs in more than 25% of the reads. Since the algorithm is aggressive in correcting for errors, it is important to align the reads to their own assembly rather than to an external reference to prevent misalignments as much as possible. RC454 uses Mosaik to align the corrected reads between each step, and as such it is required to run the script.

  • Scripture

    Scripture is a method for transcriptome reconstruction that relies solely on RNA-Seq reads and an assembled genome to build a transcriptome ab initio.

  • Siphy

    Siphy analyzes multiple sequence alignments and single outs bases or small regions that are undergoing selection by looking at reduction in substitution rates and unexpected detecting substitution patterns. A specific program to detect conserved transcription factor binding sites is also available.

  • SNAP

    SNAP is a web server for finding and annotating proxy SNPs based on linkage disequilibrium, genomic location, and coverage by commercial genotyping arrays.

  • SpectralNET

    SpectralNET is a tool to analyze networks of interactions, such as chemical-genetic networks [see also Haggarty (2003), Forman (2005)]. It is available as a standalone Windows application and as a web-enabled version.