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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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CrossMap Resource Report Resource Website 10+ mentions |
CrossMap (RRID:SCR_001173) | CrossMap | software resource | 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. | genome, assembly |
is listed by: OMICtools has parent organization: SourceForge |
PMID:24351709 | GNU General Public License | OMICS_02184 | SCR_001173 | 2026-07-25 12:04:59 | 18 | |||||||
|
Sherman Resource Report Resource Website 100+ mentions |
Sherman (RRID:SCR_001294) | Sherman | software resource | 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. | perl, bisulfite sequencing, high-throughput sequencing, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Babraham Institute |
Free, Available for download, Freely available | biotools:sherman, OMICS_02041 | http://www.bioinformatics.babraham.ac.uk/projects/sherman/ | SCR_001294 | Sherman - bisulfite-treated Read FastQ Simulator | 2026-07-25 12:04:59 | 122 | ||||||
|
GraphIBD Resource Report Resource Website |
GraphIBD (RRID:SCR_001174) | software resource | 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. | identity-by-descent, genome-wide association study |
is listed by: OMICtools has parent organization: University of California at Los Angeles; California; USA |
NHLBI K25-HL080079 | PMID:24158599 | Free, Available for download, Freely available | OMICS_02183 | SCR_001174 | 2026-07-25 12:04:56 | 0 | |||||||
|
STRViper Resource Report Resource Website 1+ mentions |
STRViper (RRID:SCR_001179) | STRViper | software resource | 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. | next-generation sequencing, short tandem repeat variation, short tandem repeat, java, unix, linux, macos, paired-end read |
is listed by: OMICtools has parent organization: University of Queensland; Brisbane; Australia |
PMID:24353318 | Free, Available for download, Freely available | OMICS_02177 | SCR_001179 | Short Tandem Repeat Variation Indentification from Paired-End Reads, STRViper: Short Tandem Repeat Variation Indentification from Paired-End Reads | 2026-07-25 12:04:56 | 1 | ||||||
|
HMMvar Resource Report Resource Website |
HMMvar (RRID:SCR_001177) | HMMvar | software resource | Software applying a quantitative prediction method to predict the effect of genetic variation using hidden Markov models. | genetic variation, insertion, deletion, indel |
is listed by: OMICtools has parent organization: Virginia Polytechnic Institute and State University; Virginia; USA |
PMID:24405700 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02181 | SCR_001177 | 2026-07-25 12:04:56 | 0 | |||||||
|
ARRmNormalization Resource Report Resource Website |
ARRmNormalization (RRID:SCR_001292) | ARRmNormalization | software resource | Software package to perform the Adaptive Robust Regression method (ARRm) for the normalization of methylation data from the Illumina Infinium HumanMethylation 450k assay. | dna methylation, microarray, preprocessing, two channel, illumina |
is listed by: OMICtools has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_02044 | SCR_001292 | ARRmNormalization - Adaptive Robust Regression normalization for Illumina methylation data | 2026-07-25 12:05:00 | 0 | |||||||
|
GenomicTools Resource Report Resource Website |
GenomicTools (RRID:SCR_001205) | GenomicTools | software resource | 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. | high-throughput sequencing, rna-seq, chip-seq, genomics, sequencing, hi-c, epigenetics, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Google Code |
PMID:22113082 | Free, Available for download, Freely available | biotools:genomictools, OMICS_02144 | https://bio.tools/genomictools | SCR_001205 | GenomicTools: a computational platform for developing high-throughput analytics in genomics. | 2026-07-25 12:04:56 | 0 | |||||
|
GenoViewer Resource Report Resource Website |
GenoViewer (RRID:SCR_001203) | GenoViewer | software resource | 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. | next-generation sequencing, sequence, mutation, windows, linux, mac os x, genome, browser, sam, bam, fasta, gff, read error, snp, mnp, insertion, deletion | is listed by: OMICtools | PMID:22359445 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02146 | https://github.com/astrid/GenoViewer | SCR_001203 | 2026-07-25 12:04:57 | 0 | ||||||
|
PARalyzer Resource Report Resource Website 1+ mentions |
PARalyzer (RRID:SCR_001208) | PARalyzer | software resource | 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. | interaction, rna-binding protein, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Duke University; North Carolina; USA |
PMID:21851591 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:paralyzer, OMICS_02137 | https://bio.tools/paralyzer | SCR_001208 | PAR-CLIP data analyzer, PARalyzer (PAR-CLIP data analyzer) | 2026-07-25 12:05:00 | 6 | |||||
|
CGH-Explorer Resource Report Resource Website 10+ mentions |
CGH-Explorer (RRID:SCR_001283) | CGH-Explorer | software resource | 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. | microarray, comparative genomic hybridization, visualization, statistics, java, windows |
is listed by: OMICtools has parent organization: University of Oslo; Oslo; Norway |
PMID:15531610 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02054 | SCR_001283 | 2026-07-25 12:04:59 | 15 | |||||||
|
methylMnM Resource Report Resource Website 1+ mentions |
methylMnM (RRID:SCR_001289) | methylMnM | software resource | 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. | dna methylation, sequencing, medip-seq, mre-seq |
is listed by: OMICtools has parent organization: Bioconductor |
GNU General Public License, v3 | OMICS_02047 | SCR_001289 | methylMnM - detect different methylation level (DMR) | 2026-07-25 12:05:00 | 9 | |||||||
|
GenoMiner Resource Report Resource Website |
GenoMiner (RRID:SCR_001202) | GenoMiner | software resource | 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 | next-generation sequencing, reference assembly, de novo assembly, chip-seq, blast, hybrid de novo assembly, hybrid reference assembly, genome, computer, hardware, instrument, equipment | is listed by: OMICtools | PMID:16267081 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02149 | http://www.astridbio.com/genominer.html | SCR_001202 | GenoMiner: Genome Analyzer | 2026-07-25 12:04:56 | 0 | |||||
|
ProbRNA Resource Report Resource Website 1+ mentions |
ProbRNA (RRID:SCR_001288) | ProbRNA | software resource | Software for computational identification of protein binding sites on RNAs using high-throughput RNA structure-probing data. | high-throughput sequencing, probe, rna structure, rna, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Chinese University of Hong Kong; Hong Kong; China |
PMID:24376038 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:probrna, OMICS_02195 | https://bio.tools/probrna | SCR_001288 | 2026-07-25 12:04:59 | 1 | ||||||
|
BlindCall Resource Report Resource Website 1+ mentions |
BlindCall (RRID:SCR_001280) | BlindCall | software resource | Software for ultra-fast base-calling of second-generation sequencing data by blind deconvolution. | base-calling, second-generation sequencing, blind deconvolution |
is listed by: OMICtools has parent organization: University of Maryland; Maryland; USA |
PMID:24413520 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02216 | SCR_001280 | 2026-07-25 12:04:59 | 1 | |||||||
|
SomaticCall Resource Report Resource Website |
SomaticCall (RRID:SCR_001196) | SomaticCall | software resource | 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. | somatic mutation, substitution, sequence, bam, mutation |
is listed by: OMICtools has parent organization: Broad Institute |
Tumor, Cancer, Normal | OMICS_02155 | SCR_001196 | 2026-07-25 12:04:57 | 0 | ||||||||
|
seq2HLA Resource Report Resource Website 1+ mentions |
seq2HLA (RRID:SCR_001199) | seq2HLA | software resource | 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. | illumina, next-generation sequencing, rna-seq, hla, hla allele, hla typing |
is listed by: OMICtools has parent organization: Johannes Gutenberg University Mainz; Rhineland-Palatinate; Germany |
BMBF | PMID:23259685 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02152 | SCR_001199 | seq2HLA - HLA typing from RNA-Seq sequence reads | 2026-07-25 12:04:57 | 2 | |||||
|
Sequedex Resource Report Resource Website 1+ mentions |
Sequedex (RRID:SCR_001233) | Sequedex | software resource | 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. | phylogenetic, function, profile, metagenomics, synthetic, dna sequence, classification, java, linux, mac os, genomic analysis, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Los Alamos National Laboratory |
PMID:22925230 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02110, biotools:sequedex | https://bio.tools/sequedex | SCR_001233 | 2026-07-25 12:04:58 | 1 | ||||||
|
PeakAnalyzer Resource Report Resource Website 1+ mentions |
PeakAnalyzer (RRID:SCR_001194) | PeakAnalyzer | software resource | 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. | genome, chip, signal peak, binding site, modification site, enrichment loci, peak region, sequence, motif, chip-seq, chip-chip, c++, java, linux, mac os x, windows, bed, gtf, annotation, r, high-throughput sequencing, chromatin binding, modification loci, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: European Bioinformatics Institute |
PMID:20691053 | Free, Available for download, Freely available | biotools:peakanalyzer, OMICS_02156 | https://bio.tools/peakanalyzer | SCR_001194 | 2026-07-25 12:04:56 | 3 | ||||||
|
BreakSeq Resource Report Resource Website 1+ mentions |
BreakSeq (RRID:SCR_001186) | BreakSeq | software resource | 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). | structural variant, breakpoint, nucleotide, fasta, gff, bowtie, genomic variation, junction mapping, insertion sequence, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Yale University; Connecticut; USA |
PMID:20037582 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:breakseq, OMICS_02168 | https://bio.tools/breakseq | SCR_001186 | Breakpoint Library and BreakSeq | 2026-07-25 12:04:57 | 1 | |||||
|
SLOPE Resource Report Resource Website |
SLOPE (RRID:SCR_001185) | SLOPE | software resource | 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. | c++, alignment, cluster, command-line, reference genome, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Utah; Utah; USA |
PMID:20876606 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02169, biotools:slope | https://bio.tools/slope | SCR_001185 | 2026-07-25 12:04:56 | 0 |
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