Searching the RRID Resource Information Network
Are you sure you want to leave this community? Leaving the community will revoke any permissions you have been granted in this community.
SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Unipro UGENE Resource Report Resource Website 100+ mentions |
Unipro UGENE (RRID:SCR_005579) | UGENE | software toolkit, software resource | A multiplatform open-source software to assist molecular biologists without much expertise in bioinformatics to manage, analyze and visualize their data. UGENE integrates widely used bioinformatics tools within a common user interface. The toolkit supports multiple biological data formats and allows the retrieval of data from remote data sources. It provides visualization modules for biological objects such as annotated genome sequences, Next Generation Sequencing (NGS) assembly data, multiple sequence alignments, phylogenetic trees and 3D structures. Most of the integrated algorithms are tuned for maximum performance by the usage of multithreading and special processor instructions. UGENE includes a visual environment for creating reusable workflows that can be launched on local resources or in a High Performance Computing (HPC) environment. UGENE is written in C++ using the Qt framework. The built-in plugin system and structured UGENE API make it possible to extend the toolkit with new functionality. | c++, windows, mac os, linux, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:22368248 DOI:10.1093/bioinformatics/bts091 |
GNU General Public License, v2, Acknowledgement requested | OMICS_01022, biotools:ugene | https://bio.tools/ugene, https://sources.debian.org/src/ugene/ | SCR_005579 | 2026-08-02 09:04:16 | 170 | ||||||
|
NGSUtils Resource Report Resource Website 10+ mentions |
NGSUtils (RRID:SCR_001236) | NGSUtils | software toolkit, software resource | A suite of software tools for analyzing and manipulating next-generation sequencing datasets, such as FASTQ, BED and BAM format files. These tools provide a stable and modular platform for data management and analysis. | mac os x, linux, next-generation sequencing, illumia, solid, 454, ion torrent, pac bio, sequencing, dna resequcing, rna resequcing, chip-seq, clip-seq, targeted resequencing, agilent exome capture, pcr targeting, dna, rna, mapping pipeline, python, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Indiana University School of Medicine; Indiana; USA |
PMID:23314324 | Free, Available for download, Freely available | biotools:ngsutils, OMICS_02104 | https://bio.tools/ngsutils | SCR_001236 | NGSUtils - Tools for next-generation sequencing analysis | 2026-08-02 09:03:04 | 38 | |||||
|
enviPick Resource Report Resource Website 1+ mentions |
enviPick (RRID:SCR_003059) | web site, software resource | Software for sequential partitioning, clustering and peak detection of centroided LC-MS mass spectrometry data (.mzXML). Interactive result and raw data plot. | standalone software, mac os x, unix/linux, windows, r |
is listed by: OMICtools has parent organization: CRAN |
Free, Available for download, Freely available | OMICS_05010 | https://rdrr.io/cran/enviPick/ | SCR_003059 | enviPick: Peak picking for high resolution mass spectrometry data | 2026-08-02 09:03:32 | 2 | |||||||
|
khmer Resource Report Resource Website 10+ mentions |
khmer (RRID:SCR_001156) | software toolkit, software resource | Software library and suite of command line tools for working with DNA sequence that takes a k-mer-centric approach to sequence analysis. It is primarily aimed at short-read sequencing data such as that produced by the Illumina platform. | dna sequence, short-read, sequencing, dna, illumina, sequence analysis, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
NHGRI R01HG007513 | PMID:26535114 DOI:10.12688/f1000research.6924.1 |
Free, Available for download, Freely available | SciRes_000166, OMICS_02560, biotools:khmer | https://github.com/dib-lab/khmer, https://bio.tools/khmer, https://sources.debian.org/src/khmer/ | https://github.com/ged-lab/khmer, http://ged.msu.edu/papers/2012-diginorm/ | SCR_001156 | khmer project, khmer - k-mer counting & filtering FTW, khmer - k-mer counting and filtering FTW, khmer: k-mer counting filtering and graph traversal FTW | 2026-08-02 09:03:00 | 25 | ||||
|
Illuminate Resource Report Resource Website 1+ mentions |
Illuminate (RRID:SCR_000178) | Illuminate | software toolkit, software resource | Python module and utilities to parse the metrics binaries output by Illumina sequencers, and provides usable data in the form of python dictionaries and dataframes. Intended to emulate the output of Illumina SAV, it allows you to print sequencing run metrics to the command line as well as work with the data programmatically. | illumina, python | is listed by: OMICtools | Free, Available for download, Freely available | OMICS_02102 | SCR_000178 | Illuminate - Analytics toolkit for Illumina sequencer metrics | 2026-08-02 09:02:48 | 1 | |||||||
|
pRESTO Resource Report Resource Website 50+ mentions |
pRESTO (RRID:SCR_001782) | pRESTO | software toolkit, software resource | Software toolkit for processing raw reads from high-throughput sequencing of lymphocyte repertoires. | lymphocyte, high throughput sequencing, processing, raw reads, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Yale School of Medicine; Connecticut; USA |
EMD/Merck/Serono ; United States-Israel Binational Science Foundation 2009046; NCRR RR19895; NLM T15 LM07056; NIAAA U19AI089992; NIAAA U19AI050864 |
PMID:24618469 | Free, Freely available | SCR_001782 | REpertoire Sequencing TOolkit | 2026-08-02 09:03:16 | 70 | ||||||
|
Apache Hadoop Resource Report Resource Website 50+ mentions |
Apache Hadoop (RRID:SCR_011879) | Hadoop | software toolkit, software resource | Software library providing a framework that allows for the distributed processing of large data sets across clusters of computers using simple programming models. It is designed to scale up from single servers to thousands of machines, each offering local computation and storage. Rather than rely on hardware to deliver high-availability, the library itself is designed to detect and handle failures at the application layer, so delivering a highly-available service on top of a cluster of computers, each of which may be prone to failures. The project includes these modules: * Hadoop Common: The common utilities that support the other Hadoop modules. * Hadoop Distributed File System (HDFS): A distributed file system that provides high-throughput access to application data. * Hadoop YARN: A framework for job scheduling and cluster resource management. * Hadoop MapReduce: A YARN-based system for parallel processing of large data sets. | computing |
is listed by: OMICtools has parent organization: Apache Software Foundation |
Open unspecified license | OMICS_01210 | SCR_011879 | 2026-08-02 09:06:04 | 57 | ||||||||
|
ALEA Resource Report Resource Website 50+ mentions |
ALEA (RRID:SCR_006417) | ALEA | software toolkit, software resource | A computational software toolbox for allele-specific (AS) epigenomics analysis. It incorporates allelic variation data within existing resources, allowing for the identification of significant associations between epigenetic modifications and specific allelic variants in human and mouse cells. It provides a customizable pipeline of command line tools for AS analysis of next-generation sequencing data (ChIP-seq, RNA-seq, etc.) that takes the raw sequencing data and produces separate allelic tracks ready to be viewed on genome browsers. ALEA takes advantage of the available genomic resources for human (The 1000 Genomes Project Consortium) and mouse (The Mouse Genome Project) to reconstruct diploid in-silico genomes for human or hybrid mice under study. Then, for each accompanying ChIP-seq or RNA-seq dataset, it generates two Wiggle track format (WIG) files from short reads aligned differentially to each haplotype. | allele, epigenomics, analysis, chip-seq, rna-seq, allelic variation, next-generation sequencing |
is listed by: OMICtools has parent organization: BC Cancer Agency |
PMID:24371156 | Academic Free License | OMICS_02193 | SCR_006417 | 2026-08-02 09:04:54 | 95 | |||||||
|
RDKit: Open-Source Cheminformatics Software Resource Report Resource Website 100+ mentions |
RDKit: Open-Source Cheminformatics Software (RRID:SCR_014274) | software toolkit, software resource | An open-source cheminformatics and machine-learning toolkit that is useable from Java or Python. It includes a collection of standard cheminformatics functionality for molecule I/O, substructure searching, chemical reactions, coordinate generation (2D or 3D), fingerprinting, etc., as well as a high-performance database cartridge for working with molecules using the PostgreSQL database. Documentation is available on the main website. | cheminformatics, machine learning, software toolkit, open source, python, c++, FASEB list |
is listed by: Debian is listed by: OMICtools |
Open source, Acknowledgement requested | OMICS_14853 | https://github.com/rdkit https://sourceforge.net/projects/rdkit/ | https://sources.debian.org/src/python3-rdkit/ | SCR_014274 | RDKit, RDKit Open-Source Cheminformatics and Machine Learning | 2026-08-02 09:06:30 | 465 | ||||||
|
Tangram Resource Report Resource Website 50+ mentions |
Tangram (RRID:SCR_006152) | software toolkit, software resource | A C / C++ command line toolbox for structural variation (SV) detection that reports mobile element insertions (MEI). It takes advantage of both read-pair and split-read algorithms and is extremely fast and memory-efficient. Powered by the Bamtools API, it can call SV events on multiple BAM files (a population) simutaneously to increase the sensitivity on low-coverage dataset. | standalone software, c, c++ | is listed by: OMICtools | PMID:25228379 | MIT License | OMICS_05785 | SCR_006152 | 2026-08-02 09:04:29 | 61 | ||||||||
|
Computational Genomics Analysis Tools Resource Report Resource Website 10+ mentions |
Computational Genomics Analysis Tools (RRID:SCR_006390) | CGAT | software toolkit, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 3, 2023. A collection of tools for the computational genomicist written in the python language to assist in the analysis of genome scale data from a range of standard file formats. The toolkit enables filtering, comparison, conversion, summarization and annotation of genomic intervals, gene sets and sequences. The tools can both be run from the Unix command line and installed into visual workflow builders, such as Galaxy. Please note that the tools are part of a larger code base also including genomics and NGS pipelines. Everyone who uses parts of the CGAT code collection is encouraged to contribute. Contributions can take many forms: bugreports, bugfixes, new scripts and pipelines, documentation, tests, etc. All contributions are welcome. | computational genomics, genomics, command-line, next-generation sequencing, python, pipeline, functional enrichment, clustering, metagenomic, contig, variant, analysis, filter, compare, conversion, summarization, annotation |
is listed by: OMICtools is related to: Galaxy has parent organization: University of Oxford; Oxford; United Kingdom |
PMID:24395753 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02209 | SCR_006390 | Computational Genomics Analysis Toolkit, CGAT - Computational Genomics Analysis Tools | 2026-08-02 09:04:36 | 28 | ||||||
|
Cluster Resource Report Resource Website 5000+ mentions |
Cluster (RRID:SCR_013505) | Cluster | software toolkit, software resource | Software R package. Methods for Cluster analysis. Performs variety of types of cluster analysis and other types of processing on large microarray datasets. | Cluster analysis, processing on large microarray datasets |
is listed by: OMICtools is listed by: Debian is listed by: SoftCite has parent organization: University of California at Berkeley; Berkeley; USA |
PMID:14871861 | Free, Available for download, Freely available | OMICS_01571 | http://www.eisenlab.org/eisen/?page_id=42, https://sources.debian.org/src/cluster3/ | SCR_013505 | Cluster 3.0 | 2026-08-02 09:06:17 | 5669 | |||||
|
Ghemical Resource Report Resource Website 10+ mentions |
Ghemical (RRID:SCR_014899) | software toolkit, software resource | Molecular modelling software package with 3D-visualization tools. It supports methods based on both molecular mechanics and quantum mechanics (using MOPAC7, and MPQC for QM). It contains geometry optimization (for MM and QM) and molecular dynamics (for MM) algorithms. | molecular modeling, 3d visualization, molecular mechanics, quantum mechanics, geometry organization, molecular dynamics |
is listed by: Debian is listed by: OMICtools |
Available for download | OMICS_21304 | https://sources.debian.org/src/ghemical/ | https://www.uku.fi/~thassine/projects/ghemical | SCR_014899 | 2026-08-02 09:06:41 | 18 | |||||||
|
Fastaq Resource Report Resource Website 10+ mentions |
Fastaq (RRID:SCR_016091) | software toolkit, software resource | Software application for diverse collection of scripts that perform useful and common FASTA/FASTQ manipulation tasks, such as filtering, merging, splitting, sorting, trimming, search/replace, etc. Input and output files can be gzipped (format is automatically detected) and individual Fastaq commands can be piped together. | diverse, script, collect, filter, merge, split, sort, trim, search, replace, file, single-letter code, nucleotide, sequence, peptide, amino acid, text-based, format |
is listed by: Debian is listed by: OMICtools has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
Free, Available for download, Freely available | OMICS_19987 | https://sources.debian.org/src/fastaq/ | SCR_016091 | 2026-08-02 09:07:11 | 25 | ||||||||
|
Fastqtl Resource Report Resource Website 100+ mentions |
Fastqtl (RRID:SCR_016093) | Fastqtl | software toolkit, software resource | Software for mapping of molecular phenotypes that implements a new permutation scheme to accurately and rapidly correct for multiple-testing at both the genotype and phenotype levels in large-scale datasets. It is used to discover quantitative trait loci, multi-dimensional genomic datasets combining DNA-seq and ChiP-/RNA-seq. | molecular, phenotype, multiply, testing, genotype, correct, genomic dataset, trait, loci, cis, quantitative, multi dimensional |
is listed by: Debian is listed by: OMICtools has parent organization: SIB Swiss Institute of Bioinformatics |
European Commission SYSCOL FP7; European Research Council ; Louis Jeantet Foundation ; Swiss National Science Foundation ; SystemsX ; NIH-NIMH (GTEx) ; Helse Sør Øst |
PMID:26708335 | Free, Available for download | OMICS_10934 | https://sources.debian.org/src/fastqtl/ | SCR_016093 | Fastqtl: Fast quantitative trait loci | 2026-08-02 09:07:14 | 127 | ||||
|
Harvest-tools Resource Report Resource Website 1+ mentions |
Harvest-tools (RRID:SCR_016132) | software toolkit, software resource | Software tools archiving and postprocessing for reference-compressed genomic multi-alignments. It is used for creating and interfacing with Gingr files, which are archives that the Harvest Suite uses to store reference-compressed multi-alignments, phylogenetic trees, filtered variants and annotations. | archiving, postprocessing, reference, compressed, genomic, multialignment, create, interface, Gingr, file, phylogentic, tree, annotation, bioinformatic, format |
is listed by: Debian is listed by: OMICtools |
Department of Homeland Security Science and Technology Directorate | PMID:25410596 | Free, Available for download, Freely available | OMICS_08468 | https://github.com/marbl/harvest-tools, https://sources.debian.org/src/harvest-tools/ | SCR_016132 | 2026-08-02 09:07:15 | 4 | ||||||
|
FastTree Resource Report Resource Website 5000+ mentions |
FastTree (RRID:SCR_015501) | software resource, source code | Source code that infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. It uses the Jukes-Cantor or generalized time-reversible (GTR) models of nucleotide evolution and the JTT, WAG, or LG models of amino acid evolution. | phylogenetic tree, phylogenetic tree creation, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools is related to: VeryFastTree |
PMID:19377059 DOI:10.1371/journal.pone.0009490 |
biotools:fasttree, OMICS_14703 | https://bio.tools/fasttree, https://sources.debian.org/src/fasttree/ | SCR_015501 | 2026-08-03 09:35:59 | 5774 | ||||||||
|
phytools Resource Report Resource Website 500+ mentions |
phytools (RRID:SCR_015502) | software resource, source code | Software R package for phylogenetic comparative biology. The package contains various functions for phylogenetic analysis of comparative data from species. | r package, phylogenetic comparison, phylogenetic analysis |
is listed by: Debian is listed by: OMICtools is hosted by: GitHub |
DOI:10.1111/j.2041-210X.2011.00169.x | Available for download, Acknowledgement requested | OMICS_12499 | https://github.com/liamrevell/phytools, https://sources.debian.org/src/r-cran-phytools/ | SCR_015502 | 2026-08-03 09:36:10 | 645 | |||||||
|
Sequence Search and Alignment by Hashing Algorithm Resource Report Resource Website 1+ mentions |
Sequence Search and Alignment by Hashing Algorithm (RRID:SCR_000544) | SSAHA2 | software resource, source code | A program designed for the efficient mapping of sequence reads onto genomic references. The software is capable of reading most sequencing platforms and giving a range of outputs are supported. | sequence, genomic, analysis, search, alignment, algorithm, mapping, bio.tools |
is listed by: OMICtools is listed by: bio.tools is related to: SMALT has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
PMID:11591649 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:ssaha2, OMICS_00690, nlx_93831 | https://bio.tools/ssaha2 | SCR_000544 | ssaha2, ssaha, Sequence Search and Alignment by Hashing Algorithm | 2026-08-03 09:31:04 | 6 | |||||
|
DecGPU Resource Report Resource Website 1+ mentions |
DecGPU (RRID:SCR_000585) | software resource | Software tool as parallel and distributed error correction algorithm for high-throughput short reads using CUDA and MPI parallel programming models. | k-mer based corrector, k-mer spectrum, illumina short read, multistage workflow, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:21447171 | Free, Available for download, Freely available | biotools:decgpu, OMICS_01101, SCR_011850, OMICS_01060 | http://musket.sourceforge.net/homepage.htm#latest, https://bio.tools/decgpu | SCR_000585 | Distributed short read Error Correction on GPUs | 2026-08-03 09:31:06 | 5 |
Can't find your Tool?
We recommend that you click next to the search bar to check some helpful tips on searches and refine your search firstly. Alternatively, please register your tool with the SciCrunch Registry by adding a little information to a web form, logging in will enable users to create a provisional RRID, but it not required to submit.
Welcome to the RRID Resources search. From here you can search through a compilation of resources used by RRID and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that RRID has compiled. You can navigate through those categories from here or change to a different tab to execute your search through. Each tab gives a different perspective on data.
If you have an account on RRID then you can log in from here to get additional features in RRID such as Collections, Saved Searches, and managing Resources.
Here is the search term that is being executed, you can type in anything you want to search for. Some tips to help searching:
If you are logged into RRID you can add data records to your collections to create custom spreadsheets across multiple sources of data.
Here are the facets that you can filter the data by.
If you have any further questions please check out our FAQs Page to ask questions and see our tutorials. Click this button to view this tutorial again.
