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:


    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.

  • 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.


    DISCOVAR is a variant caller and genome assembler that uses the latest low cost sequencing data. It can generate highly accurate variant calls for individual humans, or assemble genomes de novo.
  • Inchworm

    Inchworm assembles the RNA-Seq data into the unique sequences of transcripts, often generating full-length transcripts for a dominant isoform, but then reports just the unique portions of alternatively spliced transcripts.

  • 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.

  • 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.


    VICUNA is a de novo assembly program targeting populations with high mutation rates. It creates a single linear representation of the mixed population on which intra-host variants can be mapped. For clinical samples rich in contamination (e.g., >95%), VICUNA can leverage existing genomes, if available, to assemble only target-alike reads. After initial assembly, it can also use existing genomes to perform guided merging of contigs. For each data set (e.g., Illumina paired read, 454), VICUNA outputs consensus sequence(s) and the corresponding multiple sequence alignment of constituent reads. VICUNA efficiently handles ultra-deep sequence data with tens of thousands fold coverage.