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http://covcal.sourceforge.net/

Small and very fast utility to calculate X-coverage from Next-Generation-Sequencing data.

Proper citation: CoverageCalculator (RRID:SCR_005352) Copy   

•   Source: SciCrunch Registry

https://github.com/SciCrunch/NIF-Ontology

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.

Proper citation: NIFSTD (RRID:SCR_005414) Copy   

•   Source: SciCrunch Registry

https://www.ulisboa.pt/

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.

Proper citation: University of Lisbon; Lisbon; Portugal (RRID:SCR_005415) Copy   

•   Source: SciCrunch Registry

http://research.cs.wisc.edu/wham/

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

Proper citation: WHAM (RRID:SCR_005497) Copy   

•   Source: SciCrunch Registry

http://ccb.jhu.edu/software/FLASH/

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.

Proper citation: FLASH (RRID:SCR_005531) Copy   

•   Source: SciCrunch Registry

http://www-personal.umich.edu/~jianghui/seqmap/

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.

Proper citation: SeqMap (RRID:SCR_005495) Copy   

•   Source: SciCrunch Registry

http://www.genome.umd.edu/jellyfish.html

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.

Proper citation: Jellyfish (RRID:SCR_005491) Copy   

•   Source: SciCrunch Registry

https://github.com/mfumagalli/ngsTools

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.

Proper citation: ngsTools (RRID:SCR_005489) Copy   

•   Source: SciCrunch Registry

http://mrfast.sourceforge.net/

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

Proper citation: mrFAST (RRID:SCR_005487) Copy   

•   Source: SciCrunch Registry

http://www.oeci-eeig.org/

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

Proper citation: OECI - Organisation for European Cancer Institutes (RRID:SCR_005521) Copy   

•   Source: SciCrunch Registry

http://dna.cs.byu.edu/gnumap/

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.

Proper citation: GNUMAP (RRID:SCR_005482) Copy   

•   Source: SciCrunch Registry

http://www.ebi.ac.uk/research/enright/software/kraken

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.

Proper citation: Kraken (RRID:SCR_005484) Copy   

•   Source: SciCrunch Registry

http://enigma.ini.usc.edu/

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.

Proper citation: ENIGMA: Enhancing Neuro Imaging Genetics Through Meta-Analysis (RRID:SCR_005515) Copy   

•   Source: SciCrunch Registry

http://www.diplomatie.gouv.fr/en/

The Ministry of Foreign Affairs and is the ministry in the government of France that handles France's foreign relations.

Proper citation: French Ministry of Foreign Affairs and International Development (RRID:SCR_005518) Copy   

•   Source: SciCrunch Registry

https://alleninstitute.org/

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.

Proper citation: Allen Institute (RRID:SCR_005435) Copy   

•   Source: SciCrunch Registry

http://www.starlab.es/

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.

Proper citation: Starlab (RRID:SCR_005551) Copy   

•   Source: SciCrunch Registry

http://nebc.nerc.ac.uk/tools/bio-linux/bio-linux-7-info

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.

Proper citation: Bio-Linux (RRID:SCR_005399) Copy   

•   Source: SciCrunch Registry

http://samstat.sourceforge.net/

C software program for displaying sequence statistics for next generation sequencing. Works with large fasta, fastq and SAM/BAM files.

Proper citation: SAMStat (RRID:SCR_005432) Copy   

•   Source: SciCrunch Registry

http://mbgd.genome.ad.jp/CGAT/

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.

Proper citation: CGAT (RRID:SCR_005550) Copy   

•   Source: SciCrunch Registry

http://demo.onelaboratory.org/

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.

Proper citation: OneLab (RRID:SCR_005545) Copy   

•   Source: SciCrunch Registry