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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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CoverageCalculator Resource Report Resource Website 1+ mentions |
CoverageCalculator (RRID:SCR_005352) | CoverageCalculator | software resource | Small and very fast utility to calculate X-coverage from Next-Generation-Sequencing data. | next-generation sequencing |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_01164 | SCR_005352 | 2026-08-15 11:23:14 | 2 | |||||||||
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NIFSTD Resource Report Resource Website 10+ mentions |
NIFSTD (RRID:SCR_005414) | NIFSTD | ontology, data or information resource, controlled vocabulary | The NIF Standard Ontology (NIFSTD) is a collection of modular ontologies that provides an extensive set of terms and concepts important for the domains of neuroscience and biology, as well as the data and resources relevant for the life sciences. It is a core component of the Neuroscience Information Framework (NIF) project, a semantically enhanced portal for accessing and integrating neuroscience data, tools and information. | behavioral activity, behavioral paradigm, brain region, cell, neuron, disease, molecule, nervous system function, subcellular part, resource type, quality, brain, neuroscience, biological process, cellular anatomy, anatomy, subcellular, subcellular anatomy, organism, neurological disorder, neurologic disease, dysfunction, owl |
is listed by: BioPortal is listed by: FORCE11 is related to: NeuroLex is related to: OntoQuest is related to: InterLex has parent organization: Neuroscience Information Framework is parent organization of: NIF Cell Ontology provides: Neuron Phenotype Ontology |
PMID:18975148 PMID:22737162 |
nlx_144512 | http://bioportal.bioontology.org/ontologies/NIFSTD | https://confluence.crbs.ucsd.edu/display/NIF/Ontologies+and+Vocabularies | SCR_005414 | Neuroscience Information Framework Standard Ontology, NIF Ontology, NIF Standard, NIF-Ontology, Neuroscience Information Framework (NIF) Standard Ontology, NIF Standard Ontology, NIFSTD Ontology, NIF Ontologies | 2026-08-15 11:23:15 | 15 | |||||
|
University of Lisbon; Lisbon; Portugal Resource Report Resource Website 1+ mentions |
University of Lisbon; Lisbon; Portugal (RRID:SCR_005415) | ULisboa | university | Public research university in Lisbon, and the largest university in Portugal. It was founded in 2013, from the merger of two previous public universities located in Lisbon, the former University of Lisbon and the Technical University of Lisbon. |
is parent organization of: FuSSiMeG: Functional Semantic Similarity Measure between Gene-Products is parent organization of: ProteInOn is parent organization of: GoAnnotator is parent organization of: UNITE |
nlx_45495 | http://www.ul.pt/portal/page?_pageid=173, 1&_dad=portal&_schema=PORTAL | SCR_005415 | Lisbon University, University of Lisbon, Universidade de Lisboa | 2026-08-15 11:23:14 | 1 | ||||||||
|
WHAM Resource Report Resource Website 100+ mentions |
WHAM (RRID:SCR_005497) | WHAM | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. High-throughput sequence alignment tool that aligns short DNA sequences (reads) to the whole human genome at a rate of over 1500 million 60bps reads per hour, which is one to two orders of magnitudes faster than the leading state-of-the-art techniques. Feature list for the current version (v 0.1.5) of WHAM: * Supports paired-end reads * Supports up to 5 errores * Supports alignments with gaps * Supports quality scores for filtering invalid alignments, and sorting valid alignments * finds ALL valid alignments * Supports multi-threading * Supports rich reporting modes * Supports SAM format output | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University of Wisconsin-Madison; Wisconsin; USA |
Facebook ; NSF IIS-1110948 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00697, biotools:wham | https://bio.tools/wham, https://sources.debian.org/src/wham-align/ | SCR_005497 | Wisconsin?s High-throughput Alignment Method | 2026-08-15 11:23:15 | 345 | |||||
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FLASH Resource Report Resource Website 1000+ mentions |
FLASH (RRID:SCR_005531) | FLASh | data processing software, software application, data analysis software, software resource, sequence analysis software | Open source software tool to merge paired-end reads from next-generation sequencing experiments. Designed to merge pairs of reads when original DNA fragments are shorter than twice length of reads. Can improve genome assemblies and transcriptome assembly by merging RNA-seq data. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: shovill is related to: CLIP-Explorer has parent organization: Johns Hopkins University; Maryland; USA |
NLM R01 LM006845; NIGMS R01 GM083873; NHGRI R01 HG006677 |
PMID:21903629 | Free, Available for download, Freely available | biotools:flash, OMICS_01047 | https://sourceforge.net/projects/flashpage/files/, https://bio.tools/flash, https://sources.debian.org/src/flash/ | SCR_005531 | Fast Length Adjustment of SHort reads, Fast Length Adjustment of Short reads | 2026-08-15 11:23:16 | 2461 | ||||
|
SeqMap Resource Report Resource Website 50+ mentions |
SeqMap (RRID:SCR_005495) | SeqMap | software resource | A software tool for mapping large amount of oligonucleotide to the genome. It is designed for finding all the places in a genome where an oligonucleotide could potentially come from. SeqMap can efficiently map as many as dozens of millions of short sequences to a genome of several billions of nucleotides. While doing the mapping, several mutations as well as insertions / deletions of the nucleotide bases in the sequences can be tolerated and furthermore detected. Various input and output formats are supported, as well as many command line options for tuning almost every steps in the mapping process. A typical mapping can be done in a few hours on an ordinary PC. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University of Michigan; Ann Arbor; USA |
PMID:18697769 | Free, Non-commercial, Commercial use requires permission | biotools:seqmap, OMICS_00684 | https://bio.tools/seqmap | SCR_005495 | SeqMap - A Tool For Mapping Millions Of Short Sequences To The Genome | 2026-08-15 11:23:07 | 97 | |||||
|
Jellyfish Resource Report Resource Website 1000+ mentions |
Jellyfish (RRID:SCR_005491) | Jellyfish | software resource | A software tool for fast, memory-efficient counting of k-mers in DNA. A k-mer is a substring of length k, and counting the occurrences of all such substrings is a central step in many analyses of DNA sequence. JELLYFISH can count k-mers quickly by using an efficient encoding of a hash table and by exploiting the compare-and-swap CPU instruction to increase parallelism. Jellyfish is a command-line program that reads FASTA and multi-FASTA files containing DNA sequences. It outputs its k-mer counts in an binary format, which can be translated into a human-readable text format using the jellyfish dump command., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | c++, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University of Maryland; Maryland; USA |
PMID:21217122 DOI:10.1093/bioinformatics/btr011 |
THIS RESOURCE IS NO LONGER IN SERVICE | biotools:jellyfish, OMICS_01056 | https://bio.tools/jellyfish, https://sources.debian.org/src/jellyfish1/ | SCR_005491 | Jellyfish mer counter | 2026-08-15 11:23:07 | 1134 | |||||
|
ngsTools Resource Report Resource Website 50+ mentions |
ngsTools (RRID:SCR_005489) | ngsTools | data processing software, software application, data analysis software, software resource | A collection of software programs for population genetics analyses from NGS (Next-Generation Sequencing) data, taking into account its statistical uncertainty. The methods implemented in these programs do not rely on SNP (Single Nucleotide Polymorphism) or genotype calling, and are particularly suitable for low sequencing depth data. | java, next-generation sequencing, population, genetics, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:24458950 | GNU General Public License, v3, Acknowledgement requested | OMICS_02248, biotools:ngstools | https://bio.tools/ngstools | SCR_005489 | 2026-08-15 11:23:16 | 54 | ||||||
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mrFAST Resource Report Resource Website 10+ mentions |
mrFAST (RRID:SCR_005487) | mrFAST | software resource | Software designed to map short reads generated with the Illumina platform to reference genome assemblies; in a fast and memory-efficient mannerl. Currently Supported Features: * Output in SAM format * Indels up to 8 bp (4 bp deletions and 4 bp insertions) * Paired-end mapping ** Discordant option to generate mapping file ready for VariationHunter to detect structural variants. * One end anchored (OEA) map locations for novel sequence insertion detection with NovelSeq * Matepair library mapping (long inserts with RF orientation). Planned Features: * Multithreading | next-generation sequencing, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: SPLITREAD has parent organization: SourceForge |
PMID:19718026 | biotools:mrfast, OMICS_00671 | https://bio.tools/mrfast | SCR_005487 | mrFAST - Micro Read Fast Alignment Search Tool, Micro Read Fast Alignment Search Tool | 2026-08-15 11:23:15 | 16 | ||||||
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OECI - Organisation for European Cancer Institutes Resource Report Resource Website 1+ mentions |
OECI - Organisation for European Cancer Institutes (RRID:SCR_005521) | OECI | knowledge environment | The OECI is a non-government, non-profit organization founded in Vienna in 1979. The primary objectives of its 68 associated European Cancer Centres are to improve communication and to increase collaborative activities among European cancer institutes. These goals are achieved by promoting and strengthening Comprehensive Cancer Centres in Europe to reduce cancer incidence and mortality, and supporting cancer patients. The OECI leadership has demonstrated its active involvement in the promotion of a European approach to cancer management as a partner with UICC in the series of European Cancer Management Meetings organized with support from the European Union (Antwerp, 2000; Paris 2001). OECI members are leading Cancer Centres throughout Europe, encompassing the full spectrum of Cancer activities and national considerations. In order to facilitate the activities of their members and the definition of common programs of international interest and to facilitate the participation in European projects and programs the GEIE-LINC and the OECI in 2001 decided to set-up 9 specific Working Groups active in the following fields: Guidelines, Registration & Data Evaluation, Cost-Benefit, Pre-Clinical and Clinical Research, Education, Communication, Telematics & Telemedicine, Pathology, New Technologies | cancer | is parent organization of: OECI - Tubafrost: The European Human Frozen Tissue Bank | nlx_144618 | SCR_005521 | OECI - Organization for European Cancer Institutes, Organisation for European Cancer Institutes European Economic Interest Grouping, Organisation for European Cancer Institutes, Organization for European Cancer Institutes | 2026-08-15 11:23:16 | 1 | ||||||||
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GNUMAP Resource Report Resource Website 1+ mentions |
GNUMAP (RRID:SCR_005482) | GNUMAP | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 3rd,2023. A software program designed to accurately map sequence data obtained from next-generation sequencing machines (specifically that of Solexa/Illumina) back to a genome of any size. By using the posterior probability of mapping a given read to a specific genomic loation, we are able to account for repetitive reads by distributing them across several regions in the genome. In addition, the output of the program is created in such a way that it can be easily viewed through other free and readily- available programs. Several benchmark data sets were created with spiked-in duplicate regions, and GNUMAP was able to more accurately account for these duplicate regions. | next-generation sequencing, genome, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Brigham Young University; Utah; USA |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00664, biotools:gnumap | https://bio.tools/gnumap | SCR_005482 | Genomic Next-generation Universal MAPper | 2026-08-15 11:23:16 | 7 | ||||||
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Kraken Resource Report Resource Website 1000+ mentions |
Kraken (RRID:SCR_005484) | Kraken | software resource | A set of software tools ( Reaper, Tally and Sequence Imp) designed to streamline the analysis of next-generation sequencing data. Although designed with small RNA sequence analysis in mind the tools can be used to address issues facing next-generation sequencing in general. | adapter trimming, algorithm, next-generation sequencing, pipeline, rnaseq, sequencing |
is listed by: OMICtools has parent organization: European Bioinformatics Institute |
PMID:23816787 | Apache License | OMICS_01057 | SCR_005484 | Kraken: A set of tools for quality control and analysis of high-throughput sequence data | 2026-08-15 11:23:15 | 1906 | ||||||
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ENIGMA: Enhancing Neuro Imaging Genetics Through Meta-Analysis Resource Report Resource Website 100+ mentions |
ENIGMA: Enhancing Neuro Imaging Genetics Through Meta-Analysis (RRID:SCR_005515) | ENIGMA | data or information resource, knowledge environment, narrative resource, experimental protocol | Network that brings together researchers in imaging genomics, to understand brain structure and function, based on MRI, DTI, fMRI and genomewide association scan (GWAS) data. The ENIGMA Network has several goals: * to create a network of like-minded individuals, interested in pushing forward the field of imaging genetics * to ensure promising findings are replicated via member collaborations, in order to satisfy the mandates of most journals * to share ideas, algorithms, data, and information on promising findings or methods * to facilitate training, including workshops and conferences on key methods and emerging directions in imaging genetics. Data sharing with other members of the ENIGMA Network is optional and by no means a requirement of joining the network. Genetics and Imaging Protocols are available. | mri, dti, fmri, genomewide association scan, imaging, genetics, genomics, brain, brain structure, brain function, application, clinical neuroinformatics, genetic association, genomic analysis, imaging genomics, imputation, loni pipeline, magnetic resonance, nifti, snp, gene |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of Southern California; Los Angeles; USA |
Creative Commons License | nlx_144613 | http://www.nitrc.org/projects/enigma | http://enigma.loni.ucla.edu/ | SCR_005515 | Enhancing Neuro Imaging Genetics Through Meta-Analysis, ENIGMA Network | 2026-08-15 11:23:15 | 241 | |||||
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French Ministry of Foreign Affairs and International Development Resource Report Resource Website 1+ mentions |
French Ministry of Foreign Affairs and International Development (RRID:SCR_005518) | French MFA | institution | The Ministry of Foreign Affairs and is the ministry in the government of France that handles France's foreign relations. | is parent organization of: CIRAD | grid.454787.d, ISNI: 0000 0004 0452 4979, nlx_158286, Crossref funder ID: 501100003388, Wikidata: Q789848 | https://ror.org/00dfd1509 | SCR_005518 | 2026-08-15 11:23:16 | 1 | |||||||||
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Allen Institute Resource Report Resource Website 50+ mentions |
Allen Institute (RRID:SCR_005435) | institution | Non profit bioscience research organization in Seattle, Washington dedicated to accelerating research globally and sharing that data within the science community. Allen Institute for Brain Science, Allen Institute for Cell Science, Allen Institute for Immunology, and The Paul G. Allen Frontiers Group are four divisions of this Institute with commitment to open science model within its research institutes. | organization, brain, health, disease, research, human, mouse, dataset, cell, immunology, data, map |
is related to: scrattch taxonomy is parent organization of: Allen Institute for Brain Science is parent organization of: Allen Brain Atlas is parent organization of: Allen Human Reference Atlas, 3D, 2020 is parent organization of: Scrattch.Hicat is parent organization of: COVID-19 Open Research Dataset is parent organization of: CORD-19 Explorer is parent organization of: CellLocator is parent organization of: Allen Mouse Brain Common Coordinate Framework is parent organization of: Common Cell Type Nomenclature is parent organization of: Smart-seq2 Single Nucleus Multi Sample Pipeline is parent organization of: BICCN is parent organization of: Allen Cell and Structure Segmenter is parent organization of: Allen Brain Cell Atlas is parent organization of: BRAIN Initiative Cell Atlas Network is parent organization of: MapMyCells is parent organization of: Genetic Tools Atlas is parent organization of: Annotation Comparison Explorer is parent organization of: BioFile Finder is parent organization of: HMBA Adult Human Brain Atlas is parent organization of: Harmonized Ontology of Mammalian Brain Anatomy (HOMBA) |
nlx_144532, Wikidata:Q24191489, grid.507729.e | https://ror.org/03cpe7c52 | SCR_005435 | The Allen Institute | 2026-08-15 11:23:15 | 61 | ||||||||
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Starlab Resource Report Resource Website 50+ mentions |
Starlab (RRID:SCR_005551) | Starlab | commercial organization | Starlab''s mission is to transform science into technologies with a profound and positive impact on society. We achieve this by identifying social needs and the market opportunities they create. Then we reach to science and engineering to propose or provide technical solutions, products and services for governments, industry and downstream markets. Starlab Research carries out interdisciplinary R&D focusing on two areas: Space and Applied Neuroscience. Our vision is to make science more useful, alive, vibrant, faster. Our staff consists of a team of scientists, engineers and economists from different nationalities working together to provide our clients with breakthrough technologies that create business opportunities. The growing Starlab team (now more than 28 on staff) includes 5 nationalities spanning knowledge in physics, engineering, oceanography, computer science, neuroscience and economics. Circa 50% of our staff have a PhD, and more than 80% a Master or PhD. We target technology and applications: the development of new sensors and efficient algorithms to extract information from data, identification of platforms and deployment opportunities, as well as the development of services and products. Interdisciplinarity is a key aspect of our research. Space R&D develops payloads, algorithms and mission feasibility studies. We have demonstrated experience in GNSS technologies, radar altimetry and space astronomy. Earth Observation applications include technologies such as GNSS-R, SAR and multi-spectral analysis for environmental and energy applications. We have demonstrated expertise in the development of innovative sensors and systems in both the Space and Applied Neuroscience areas, signal-processing algorithms, with a strong specialization in electrophysiology algorithms, software and hardware. It will also manage the project and prospect potential commercial impact. | neuroscience, space | is parent organization of: HC2: Human-Computer Confluence | grid.32517.32, nlx_144642 | https://ror.org/040cxgs87 | SCR_005551 | Starlab - Living Science, Starlab - Where science turns into the technologies of the future | 2026-08-15 11:23:15 | 99 | |||||||
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Bio-Linux Resource Report Resource Website 10+ mentions |
Bio-Linux (RRID:SCR_005399) | Bio-Linux | software resource | A free, fully featured, powerful, configurable and easy to maintain bioinformatics workstation that provides more than 500 bioinformatics programs on an Ubuntu Linux 12.04 LTS base. Install it or run it live. There is a graphical menu for bioinformatics programs, as well as easy access to the Bio-Linux bioinformatics documentation system and sample data useful for testing programs. You can run a Bio-Linux system on Amazon EC2 or other cloud computing architectures by using CloudBioLinux. | ubuntu, cloud computing, workstation, bioinformatics |
is recommended by: NERC Environmental Bioinformatics Centre is listed by: OMICtools has parent organization: Natural Environment Research Council |
PMID:16841067 | Acknowledgement requested, Open unspecified license | OMICS_01137 | SCR_005399 | BioLinux, NEBC Bio-Linux | 2026-08-15 11:23:14 | 33 | ||||||
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SAMStat Resource Report Resource Website 10+ mentions |
SAMStat (RRID:SCR_005432) | SAMStat | software resource | C software program for displaying sequence statistics for next generation sequencing. Works with large fasta, fastq and SAM/BAM files. | sequence statistic, c, next generation sequencing, fasta file, fastq file, sam file, bam file, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: RIKEN Yokohama Institute; Kanagawa; Japan |
PMID:21088025 | Acknowledgement requested | biotools:samstat, OMICS_01073 | https://bio.tools/samstat | SCR_005432 | 2026-08-15 11:23:14 | 39 | ||||||
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CGAT Resource Report Resource Website 1+ mentions |
CGAT (RRID:SCR_005550) | CGAT | software resource | A comparative genome analysis tool for detailed comparison of closely related bacterial-sized genomes. It visualizes precomputed pairwise genome alignments on both dotplot and alignment viewers. Users can add information on this alignment, such as existence of tandem repeats or interspersed repetitive sequences and changes in codon usage bias, to facilitate interpretation of the observed genomic changes. Besides visualization functionalities, it also provides a general framework to process genome-scale alignments using various existing alignment programs. CGAT employs a client-server architecture, which consists of AlignmentViewer (client; a Java application) and DataServer (a set of Perl scripts). The DataServer package contains data construction scripts and CGI scripts and the AlignmentViewer program visualizes the alignment data obtained from the server thorough the HTTP protocol. | genome, alignment, visualizing, evolution, dotplot |
is listed by: OMICtools has parent organization: National Institute for Basic Biology; Okazaki; Japan |
PMID:17062155 | OMICS_00930 | SCR_005550 | CGAT - A Comparative Genome Analysis Tool, Comparative Genome Analysis Tool | 2026-08-15 11:23:16 | 3 | |||||||
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OneLab Resource Report Resource Website 1+ mentions |
OneLab (RRID:SCR_005545) | OneLab | data repository, storage service resource, portal, data or information resource, community building portal, service resource |
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 24, 2017. Platform to enable dissemination of scientific findings, foster open peer commentary and promote collaboration among the research community. Widespread participation in OneLab will increase the quality, transparency and reproducibility of data thus accelerating the pace of scientific discoveries. The result will be a streamlined process from the bench to the clinic with tremendous benefits for the well-being of the general public. OneLab is a private professional network that mirrors the hierarchy of real world research laboratories. Users are designated as either principal investigators (PI) or lab members. PIs can invite lab members to join and data posted by lab members cannot be shared without PI approval. In this way the PI retains FULL CONTROL over the dissemination of scientific content thus safeguarding the primacy of authorship. This professional network will serve as a backdrop for sharing scientific findings, promote collaborations, and provide a basis for open peer commentary. Semantic Search of Structured Content OneLab implements a powerful search functionality that is based on structured content. Users describe their Single Figure Posts (SFPs) using defined fields such as model organism, genes, proteins and assay. This additional layer of structure provides the basis for a smarter and more accurate search engine that understands searcher intent and therefore generates more relevant results. Structured content allows OneLab to go one step further by offering recommendations based on similarities that might not be intuitive, thus increasing potential collaborations among scientists., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. |
data sharing, semantics, collaboration, down syndrome | has parent organization: University of California at San Diego; California; USA | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_144637 | SCR_005545 | OneLab - accelerating discoveries, One Lab | 2026-08-15 11:23:08 | 4 |
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