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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://bionimbus.opensciencedatacloud.org/

A cloud-based infrastructure for managing, analyzing and sharing genomics datasets.

Proper citation: Bionimbus (RRID:SCR_001189) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/RCASPAR.html

Software package for survival time prediction based on a piecewise baseline hazard Cox regression model. It is meant to help predict survival times in the presence of high-dimensional explanatory covariates.

Proper citation: RCASPAR (RRID:SCR_001253) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/CNVtools.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software package to facilitate the testing of Copy Number Variant data for genetic association, typically in case-control studies.

Proper citation: CNVtools (RRID:SCR_001250) Copy   

•   Source: SciCrunch Registry

http://med.stanford.edu/tanglab/software/saber.html

Software program suitable for genome-scale data which uses a Markov-hidden Markov model (MHMM) to estimate local ancestry. The MHMM makes it possible to identify genomic blocks of a particular ancestry by use of any high-density single-nucleotide-polymorphism panel. One application is to perform admixture mapping without genotyping special ancestry-informative-marker panels.

Proper citation: SABER (RRID:SCR_001257) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/multtest.html

Software package for non-parametric bootstrap and permutation resampling-based multiple testing procedures (including empirical Bayes methods) for controlling the family-wise error rate (FWER), generalized family-wise error rate (gFWER), tail probability of the proportion of false positives (TPPFP), and false discovery rate (FDR). Several choices of bootstrap-based null distribution are implemented (centered, centered and scaled, quantile-transformed). Single-step and step-wise methods are available. Tests based on a variety of t- and F-statistics (including t-statistics based on regression parameters from linear and survival models as well as those based on correlation parameters) are included. When probing hypotheses with t-statistics, users may also select a potentially faster null distribution which is multivariate normal with mean zero and variance covariance matrix derived from the vector influence function. Results are reported in terms of adjusted p-values, confidence regions and test statistic cutoffs. The procedures are directly applicable to identifying differentially expressed genes in DNA microarray experiments.

Proper citation: multtest (RRID:SCR_001255) Copy   

•   Source: SciCrunch Registry

https://github.com/pmelsted/BFCounter

Software program for counting k-mers in DNA sequence data. It identifies all the k-mers that occur more than once in a DNA sequence data set using a Bloom filter, a probabilistic data structure that stores all the observed k-mers implicitly in memory with greatly reduced memory requirements.

Proper citation: BFCounter (RRID:SCR_001248) Copy   

•   Source: SciCrunch Registry

https://github.com/grenaud/freeIbis

A software basecaller for Illumina sequencers with calibrated quality scores.

Proper citation: freeIbis (RRID:SCR_001241) Copy   

•   Source: SciCrunch Registry

http://www.zbh.uni-hamburg.de/?id=211

A collection of flexible and memory-efficient software programs for k-mer counting and indexing of large sequence sets. It is based on enhanced suffix arrays which gives a much larger flexibility concerning the choice of the k-mer size. It can process large data sizes of several billion bases.

Proper citation: TALLYMER (RRID:SCR_001244) Copy   

•   Source: SciCrunch Registry

http://www.ebi.ac.uk/~stijn/reaper/tally.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software program for deduplicating sequence fragments. It minimises memory usage by compressing sequences and using compact memory allocation techniques. A built-in parser allows a variety of input file formats and a simple specification language allows flexible output file formats. It can be made aware of paired-end reads, and it can handle degenerate sequence inserts intended to reveal amplification biases. Tally comes with reaper, a program for demultiplexing, trimming and filtering short read sequencing data.

Proper citation: Tally (RRID:SCR_001239) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/ITALICS.html

Software package to normalize of Affymetrix GeneChip Human Mapping 100K and 500K set.

Proper citation: ITALICS (RRID:SCR_001274) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/2.14/bioc/html/mBPCR.html

Software package that estimates the DNA copy number profile to detect regions with copy number changes.

Proper citation: mBPCR (RRID:SCR_001273) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/devel/bioc/html/CGHregions.html

Software package for dimension Reduction for Array CGH Data with Minimal Information Loss.

Proper citation: CGHregions (RRID:SCR_001278) Copy   

•   Source: SciCrunch Registry

http://bioconductor.org/packages/release/bioc/html/quantsmooth.html

Software package for quantile smoothing and genomic visualization of array data.

Proper citation: quantsmooth (RRID:SCR_001271) Copy   

•   Source: SciCrunch Registry

http://pfind.ict.ac.cn/se/plink/

Software dedicated for the analysis of chemically cross-linked proteins or protein complexes using mass spectrometry., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: pFind Studio: pLink (RRID:SCR_000084) Copy   

•   Source: SciCrunch Registry

http://www.tm4.org/spotfinder.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Software designed for the rapid, reproducible and computer-aided analysis of microarray images and the quantification of gene expression.

Proper citation: Spotfinder (RRID:SCR_000085) Copy   

•   Source: SciCrunch Registry

http://biolemmatizer.sourceforge.net/

A domain-specific lemmatization software tool for the morphological analysis of biomedical literature.

Proper citation: BioLemmatizer (RRID:SCR_000117) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/ReQON.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Algorithm for recalibrating the base quality scores for aligned sequencing data in BAM format.

Proper citation: ReQON (RRID:SCR_000075) Copy   

•   Source: SciCrunch Registry

http://www.iro.umontreal.ca/~csuros/quadgt/

Software package for calling single-nucleotide variants in four sequenced genomes comprising a normal-tumor pair and the two parents. Genotypes are inferred using a joint model of parental variant frequencies, de novo germline mutations, and somatic mutations. The model quantifies the descent-by-modification relationships between the unknown genotypes by using a set of parameters in a Bayesian inference setting. Note that you can use it on any subset of the four related genomes, including parent-offspring trios, and normal-tumor pairs without parental samples.

Proper citation: QuadGT (RRID:SCR_000073) Copy   

•   Source: SciCrunch Registry

http://soap.genomics.org.cn/soapfuse.html

THIS RESOURCE IS NO LONGER IN SERVICE.Documented on August 23,2022. An open source tool developed for genome-wide detection of fusion transcripts from human being paired-end RNA-Seq data. This tool is a part of a larger set of tools to efficiently align oligonucleotides onto reference sequences .

Proper citation: SOAPfuse (RRID:SCR_000078) Copy   

•   Source: SciCrunch Registry