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http://crossmap.sourceforge.net/

A software program for convenient conversion of genome coordinates (or annotation files) between different assemblies. It supports most commonly used file formats including SAM/BAM, Wiggle/BigWig, BED, GFF/GTF, VCF. It is designed to liftover genome coordinates between assemblies. It?s not a program for aligning sequences to reference genome. CrossMap is not recommend for converting genome coordinates between species.

Proper citation: CrossMap (RRID:SCR_001173) Copy   

•   Source: SciCrunch Registry

https://github.com/FelixKrueger/Sherman

Software tool to simulate FastQ files for high-throughput sequencing experiments. It allows the user to introduce various "contaminants" into the sequences, such as basecall errors, SNPs, adapter fragments etc., in order to evaluate the influence of common problems observed in many Next-Gen Sequencing experiments.

Proper citation: Sherman (RRID:SCR_001294) Copy   

•   Source: SciCrunch Registry

http://genetics.cs.ucla.edu/graphibd/

Identity-by-descent (IBD) association testing software for genome-wide association study analysis. It requires an IBD detection method such as Beagle FastIBD to run first. GraphIBD then builds upon the IBD information to test if the IBD segments show association to the traits.

Proper citation: GraphIBD (RRID:SCR_001174) Copy   

•   Source: SciCrunch Registry

http://bioinf.scmb.uq.edu.au/STRViper/

Software tool for detection of short tandem repeat (STR) variations from paired-end next generation sequencing data. It makes variant calls based on deviations in sequence fragment sizes, allowing the analysis of repeats of size up to fragment length. This stratergy also helps avoiding false calls resulting from errors arised from sequencing of repeat DNA.

Proper citation: STRViper (RRID:SCR_001179) Copy   

•   Source: SciCrunch Registry

https://bioinformatics.cs.vt.edu/zhanglab/hmm/

Software applying a quantitative prediction method to predict the effect of genetic variation using hidden Markov models.

Proper citation: HMMvar (RRID:SCR_001177) Copy   

•   Source: SciCrunch Registry

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

Software package to perform the Adaptive Robust Regression method (ARRm) for the normalization of methylation data from the Illumina Infinium HumanMethylation 450k assay.

Proper citation: ARRmNormalization (RRID:SCR_001292) Copy   

•   Source: SciCrunch Registry

https://code.google.com/p/ibm-cbc-genomic-tools/

A flexible computational platform, comprising both a command-line set of tools and a C++ API, for the analysis and manipulation of high-throughput sequencing data such as DNA-seq, RNA-seq, ChIP-seq and MethylC-seq. It implements a variety of mathematical operations between sets of genomic regions thereby enabling the prototyping of computational pipelines that can address tasks from preprocessing and quality control to meta-analyses. The user can create average read profiles across transcriptional start sites or enhancer sites, quickly prototype customized peak discovery methods for ChIP-seq experiments, perform genome-wide statistical tests such as enrichment analyses, design controls via appropriate randomization schemes, among other applications. In addition to enabling rapid prototyping, the platform is designed to analyze large-datasets in a single-pass fashion in order to minimize memory and intermediate file requirements. The platform supports the widely used BED format to facilitate visualization as well as integration with existing platforms and pipelines such as Galaxy or BioConductor.

Proper citation: GenomicTools (RRID:SCR_001205) Copy   

•   Source: SciCrunch Registry

http://www.genoviewer.com/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Open source viewer / browser software for the SAM / BAM format commonly used in the assembly tasks of Next Generation Sequencing data.

Proper citation: GenoViewer (RRID:SCR_001203) Copy   

•   Source: SciCrunch Registry

http://www.genome.duke.edu/labs/ohler/research/PARalyzer/

Software tool to generate a high resolution map of interaction sites between RNA-binding proteins and their targets. The algorithm utilizes the deep sequencing reads generated by the newly developed PAR-CLIP (Photoactivatable-Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation) protocol. The use of photoactivatable nucleotides in the PAR-CLIP protocol results in a more efficient crosslinking between the RNA-binding protein and its target relative to other CLIP methods; in addition a nucleotide substitution occurs at the site of crosslinking during Illumina library preparation. PARalyzer utilizes this nucleotide substition in a kernel density estimate classifier to generate the high resolution set of Protein-RNA interaction sites.

Proper citation: PARalyzer (RRID:SCR_001208) Copy   

•   Source: SciCrunch Registry

http://heim.ifi.uio.no/bioinf/Projects/CGHExplorer/

Software program for visualization and statistical analysis of microarray-based comparative genomic hybridization (array-CGH) data. The program has preprocessing facilities, tools for graphical exploration of individual arrays or groups of arrays, and tools for statistical identification of regions of amplification and deletion.

Proper citation: CGH-Explorer (RRID:SCR_001283) Copy   

•   Source: SciCrunch Registry

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

Software package to detect different methylation levels (DMR) that gives the exact p-value and q-value of MeDIP-seq and MRE-seq data for different samples comparison.

Proper citation: methylMnM (RRID:SCR_001289) Copy   

•   Source: SciCrunch Registry

http://astridbio.com/genominer-genome-analyzer/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. A next generation sequencing data analysis computer for biologists with or without IT background. It has an easy to-use graphical interface to analyze sequencing data in with only 15 clicks. A range of standard, add-on and custom applications help analyze and visualize data generated by Next Generation Sequencing machines. These are installed on each GenoMiner by default: * Reference assembly * De novo assembly * ChiP-Seq * BLAST * Hybrid de novo assembly * Hybrid reference assembly Add-on applications: * Quality assesment * RNA-Seq * Copy Number Variation (CNV) * Multiple Sequence Alignment * miRNA-Seq * Variant Calling

Proper citation: GenoMiner (RRID:SCR_001202) Copy   

•   Source: SciCrunch Registry

http://yiplab.cse.cuhk.edu.hk/probrna/

Software for computational identification of protein binding sites on RNAs using high-throughput RNA structure-probing data.

Proper citation: ProbRNA (RRID:SCR_001288) Copy   

•   Source: SciCrunch Registry

http://cbcb.umd.edu/~hcorrada/secgen/

Software for ultra-fast base-calling of second-generation sequencing data by blind deconvolution.

Proper citation: BlindCall (RRID:SCR_001280) Copy   

•   Source: SciCrunch Registry

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

Software program that finds single-base differences (substitutions) between sequence data from tumor and matched normal samples. It is designed to be highly stringent, so as to achieve a low false positive rate. It takes as input a BAM file for each sample, and produces as output a list of differences (somatic mutations). Note: This software package is no longer supported and information on this page is provided for archival purposes only.

Proper citation: SomaticCall (RRID:SCR_001196) Copy   

•   Source: SciCrunch Registry

http://tron-mainz.de/tron-facilities/computational-medicine/seq2hla/

Software for obtaining an individualXs HLA class I and II type and expression using standard NGS (Next-generation sequencing) RNA-Seq data. It comprises mapping RNA-Seq reads against a reference database of HLA alleles, determining and reporting HLA type, confidence score and locus-specific expression level.

Proper citation: seq2HLA (RRID:SCR_001199) Copy   

•   Source: SciCrunch Registry

http://sequedex.lanl.gov/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 18,2025.Software to classify the function and phylogeny of reads as short as 30 bp. It is flexible, which can utilize multiple data modules and downstream analysis scripts. It is fast, reading in signature lists of 5-500 million peptide signatures in 1-15 minutes, and subsequently processes genomic fragments at the rate of 6 Gbp/hr. It parallelizes without significant increase in memory requirements until I/O bound on multiple input files; parallelization works well on 64 processors.

Proper citation: Sequedex (RRID:SCR_001233) Copy   

•   Source: SciCrunch Registry

http://www.bioinformatics.org/peakanalyzer/wiki/

A set of standalone software programs for the automated processing of any genomic loci, with an emphasis on datasets consisting of ChIP-derived signal peaks. The software is able to identify individual binding / modification sites from enrichment loci, retrieve peak region sequences for motif discovery, and integrate experimental data with different classes of annotated elements throughout the genome. PeakAnalyzer requires a peak file and a feature annotation file in BED or GTF format. Complete annotation files for the current builds of the human (HG19) and mouse (MM9) genomes are provided with the software distribution.

Proper citation: PeakAnalyzer (RRID:SCR_001194) Copy   

•   Source: SciCrunch Registry

http://sv.gersteinlab.org/breakseq/

Software for scanning reads from short-read sequenced genomes against a human breakpoint library to accurately identify structural variants (SVs). The library of breakpoints at nucleotide resolution were assembled from collating and standardizing ~2,000 published structural variants (SVs). For each breakpoint, its ancestral state (through comparison to primate genomes) was inferred and its mechanism of formation (e.g., nonallelic homologous recombination, NAHR).

Proper citation: BreakSeq (RRID:SCR_001186) Copy   

•   Source: SciCrunch Registry

http://www-genepi.med.utah.edu/suppl/SLOPE/index.html

Software that consists of two command-line utilities, slope_align (which finds the best split-read alignments to the reference genome) and slope_cluster (which clusters and outputs the alignments)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: SLOPE (RRID:SCR_001185) Copy   

•   Source: SciCrunch Registry