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http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_genotyper_UnifiedGenotyper.html

A multiple-sample, technology-aware SNP and indel caller.

Proper citation: UnifiedGenotyper (RRID:SCR_004710) Copy   

•   Source: SciCrunch Registry

http://www.broadinstitute.org/igv/

A high-performance visualization tool for interactive exploration of large, integrated genomic datasets.

Proper citation: Integrative Genomics Viewer (RRID:SCR_011793) Copy   

•   Source: SciCrunch Registry

http://www.broadinstitute.org/mpg/magenta/

A computational tool that tests for enrichment of genetic associations in predefined biological processes or sets of functionally related genes, using genome-wide genetic data as input.

Proper citation: MAGENTA (RRID:SCR_003422) Copy   

•   Source: SciCrunch Registry

http://www.broadinstitute.org/scientific-community/science/programs/cancer/ultrasome

An efficient methodology for detecting and delineating gains and losses of chromosomal material in DNA copy-number data.

Proper citation: Ultrasome (RRID:SCR_008465) Copy   

•   Source: SciCrunch Registry

http://www.broadinstitute.org/cancer/cga/invex/

A permutation-based method (written in Python) for ascertaining genes with a somatic mutation distribution showing evidence of positive selection for non-silent mutations.

Proper citation: InVEx (RRID:SCR_008734) Copy   

•   Source: SciCrunch Registry

http://trinityrnaseq.sourceforge.net/

Software for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data.

Proper citation: Trinity (RRID:SCR_013048) Copy   

•   Source: SciCrunch Registry

http://www.broadinstitute.org/annotation/medea/

THIS RESOURCE IS NO LONGER IN SERVCE, documented June, 2019.Comparative Genomic Visualization with Adobe Flash.

Proper citation: MEDEA (RRID:SCR_013356) Copy   

•   Source: SciCrunch Registry

http://www.broadinstitute.org/cancer/cga/mutsig

Software that analyzes lists of mutations discovered in DNA sequencing, to identify genes that were mutated more often than expected by chance given background mutation processes.

Proper citation: MutSig (RRID:SCR_010779) Copy   

•   Source: SciCrunch Registry

https://www.broadinstitute.org/scientific-community/science/programs/genome-sequencing-and-analysis/computational-rd/computational-

Software tool as whole genome shotgun assembler that can generate high quality genome assemblies using short reads (~100bp) such as those produced by the new generation of sequencers.

Proper citation: ALLPATHS-LG (RRID:SCR_010742) Copy   

•   Source: SciCrunch Registry

http://www.broadinstitute.org/genome_bio/siphy/

Software that implements rigorous statistical tests to detect bases under selection from a multiple alignment data. It takes full advantage of deeply sequenced phylogenies to estimate both unlikely substitution patterns as well as slowdowns or accelerations in mutation rates. It can be applied as an Hidden Markov Model (HMM), in sliding windows, or to specific regions.

Proper citation: SiPhy (RRID:SCR_000564) Copy   

•   Source: SciCrunch Registry

http://www.broadinstitute.org/cancer/cga/contest

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 8,2025. A software tool (and method) for estimating the amount of cross-sample contamination in next generation sequencing data.

Proper citation: ContEst (RRID:SCR_000595) Copy   

•   Source: SciCrunch Registry

http://www.broadinstitute.org/science/programs/genome-biology/computational-rd/vaal-manual

A polymorphism discovery algorithm for short reads. To run it, you provide reads (and quality scores) from a "sample genome" as input, along with a vector sequence to trim from the reads, and a reference sequence for a related genome to compare to. VAAL produces as output a an assembly for the sample genome, together with a mask showing which bases are "trusted". It then deduces from that a list of differences between the sample and related genomes. Alternatively, it can be provided as input read data for two sample genomes, together with a reference sequence for a related genome. In this case, VAAL produces assemblies for each of the sample genomes, and compares them to each other, thereby deducing a list of differences between them. VAAL has been tested on bacteria, using single lanes of 36 bp unpaired reads from the Illumina platform. Note: This software package is no longer supported and information on this page is provided for archival purposes only.

Proper citation: VAAL (RRID:SCR_001184) Copy   

•   Source: SciCrunch Registry

http://www.broadinstitute.org/science/programs/genome-biology/computational-rd/computational-research-and-development

A software for genome assembly, and is specifically designed to analyze long Sanger-chemistry reads.

Proper citation: ARACHNE (RRID:SCR_000351) Copy   

•   Source: SciCrunch Registry

http://www.broadinstitute.org/scientific-community/science/projects/viral-genomics/v-phaser-2

A software tool to call variants in genetically heterogeneous populations from ultra-deep sequence data. It combines information regarding the covariation (i.e. phasing) between observed variants to increase sensitivity and an expectation maximization algorithm that iteratively recalibrates base quality scores to increase specificity. V-Phaser can reliably detect rare variants in diverse populations that occur at frequencies of <1%. V-Phaser 2 is a complete rewrite of the original V-Phaser. It contains a new model for length polymorphisms (indels) and incorporates paired end read information in its phasing model. The data access and probability computation sections of the code have also been highly optimized, resulting in substantial improvements in running time and memory usage.

Proper citation: V-Phaser 2 (RRID:SCR_005212) Copy   

•   Source: SciCrunch Registry

http://www.broadinstitute.org/cancer/cga/absolute

Software to estimate purity / ploidy, and from that compute absolute copy-number and mutation multiplicities. When DNA is extracted from an admixed population of cancer and normal cells, the information on absolute copy number per cancer cell is lost in the mixing. The purpose of ABSOLUTE is to re-extract these data from the mixed DNA population. This process begins by generation of segmented copy number data, which is input to the ABSOLUTE algorithm together with pre-computed models of recurrent cancer karyotypes and, optionally, allelic fraction values for somatic point mutations. The output of ABSOLUTE then provides re-extracted information on the absolute cellular copy number of local DNA segments and, for point mutations, the number of mutated alleles.

Proper citation: ABSOLUTE (RRID:SCR_005198) Copy   

•   Source: SciCrunch Registry

http://www.broadinstitute.org/cancer/cga/indelocator

A software tool for calling short indels in next generation sequencing data.

Proper citation: Indelocator (RRID:SCR_005258) Copy   

•   Source: SciCrunch Registry

http://www.broadinstitute.org/software/scripture/

Software for transcriptome reconstruction that relies solely on RNA-Seq reads and an assembled genome to build a transcriptome ab initio. The statistical methods to estimate read coverage significance are also applicable to other sequencing data. Scripture also has modules for ChIP-Seq peak calling.

Proper citation: Scripture (RRID:SCR_005269) Copy   

•   Source: SciCrunch Registry

http://www.broadinstitute.org/software/syzygy/

A targeted sequencing post processing analysis software tool that allows: 1. SNP and indel detection; 2. Allele frequency estimation; 3. Single-marker association test; 4. Group-wise marker test association; 5. Experimental QC summary (%dbSNP, Ts/Tv, Ns/S); 6. Power to detect variant. (entry from Genetic Analysis Software)

Proper citation: SYZYGY (RRID:SCR_002157) Copy   

•   Source: SciCrunch Registry

https://software.broadinstitute.org/gatk/

A software package to analyze next-generation resequencing data. The toolkit offers a wide variety of tools, with a primary focus on variant discovery and genotyping as well as strong emphasis on data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size. This software library makes writing efficient analysis tools using next-generation sequencing data very easy, and second it's a suite of tools for working with human medical resequencing projects such as 1000 Genomes and The Cancer Genome Atlas. These tools include things like a depth of coverage analyzers, a quality score recalibrator, a SNP/indel caller and a local realigner. (entry from Genetic Analysis Software)

Proper citation: GATK (RRID:SCR_001876) Copy   

•   Source: SciCrunch Registry

http://www.broadinstitute.org/mpg/snap/

A computer program and web-based service for the rapid retrieval of linkage disequilibrium proxy single nucleotide polymorphism (SNP) results given input of one or more query SNPs and based on empirical observations from the International HapMap Project and the 1000 Genomes Project. A series of filters allow users to optionally retrieve results that are limited to specific combinations of genotyping platforms, above specified pairwise r2 thresholds, or up to a maximum distance between query and proxy SNPs. SNAP can also generate linkage disequilibrium plots

Proper citation: SNAP - SNP Annotation and Proxy Search (RRID:SCR_002127) Copy   

•   Source: SciCrunch Registry