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http://www.re3data.org/

Global registry of research data repositories from all academic disciplines that allows the easy identification of appropriate research data repositories, both for data producers and users. Information icons display principal attributes of a repository that can be used for multi-faceted searches. Repository operators can suggest their infrastructures to be listed via a simple application form. A repository is indexed when the minimum requirements are met, i.e. mode of access to the data and repository, as well as the terms of use.

Proper citation: re3data.org (RRID:SCR_006782) Copy   

•   Source: SciCrunch Registry

https://www.sanger.ac.uk/science/tools/reapr

Software tool to identify errors in genome assemblies without need for reference sequence. Can be used in any stage of assembly pipeline to automatically break incorrect scaffolds and flag other errors in assembly for manual inspection. Reports mis-assemblies and other warnings, and produces new broken assembly based on error calls.

Proper citation: Recognition of Errors in Assemblies using Paired Reads (RRID:SCR_017625) Copy   

•   Source: SciCrunch Registry

https://github.com/hemberg-lab/scmap

Software tool for unsupervised projection of single cell RNA-seq data. Used for projecting cells from scRNA-seq data set onto cell types or individual cells from other experiments.

Proper citation: Scmap (RRID:SCR_017338) Copy   

•   Source: SciCrunch Registry

http://www.sanger.ac.uk/cgi-bin/teams/team30/arnie

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 1,2023. Database that integrates the extracellular protein interaction network generated in our lab using AVEXIS technology with spatiotemporal expression patterns for all genes in the network. The tool allows users to browse the network by clicking on individual proteins, or by specifying the spatiotemporal parameters. Clicking on connector lines will allow users to compare stage-matched expression patterns for genes encoding interacting proteins. Additionally, users can rapidly search for their genes in the network using the BLAST server provided.

Proper citation: ARNIE (RRID:SCR_000514) Copy   

•   Source: SciCrunch Registry

http://cancer.sanger.ac.uk/cancergenome/projects/cosmic/

Database to store and display somatic mutation information and related details and contains information relating to human cancers. The mutation data and associated information is extracted from the primary literature. In order to provide a consistent view of the data a histology and tissue ontology has been created and all mutations are mapped to a single version of each gene. The data can be queried by tissue, histology or gene and displayed as a graph, as a table or exported in various formats.
Some key features of COSMIC are:
* Contains information on publications, samples and mutations. Includes samples which have been found to be negative for mutations during screening therefore enabling frequency data to be calculated for mutations in different genes in different cancer types.
* Samples entered include benign neoplasms and other benign proliferations, in situ and invasive tumours, recurrences, metastases and cancer cell lines.

Proper citation: COSMIC - Catalogue Of Somatic Mutations In Cancer (RRID:SCR_002260) Copy   

•   Source: SciCrunch Registry

http://www.genes2cognition.org/

A neuroscience research program that studies genes, the brain and behavior in an integrated manner, established to elucidate the molecular mechanisms of learning and memory, and shed light on the pathogenesis of disorders of cognition. Central to G2C investigations is the NMDA receptor complex (NRC/MASC), that is found at the synapses in the central nervous system which constitute the functional connections between neurons. Changes in the receptor and associated components are thought to be in a large part responsible for the phenomenon of synaptic plasticity, that may underlie learning and memory. G2C is addressing the function of synapse proteins using large scale approaches combining genomics, proteomics and genetic methods with electrophysiological and behavioral studies. This is incorporated with computational models of the organization of molecular networks at the synapse. These combined approaches provide a powerful and unique opportunity to understand the mechanisms of disease genes in behavior and brain pathology as well as provide fundamental insights into the complexity of the human brain. Additionally, Genes to Cognition makes available its biological resources, including gene-targeting vectors, ES cell lines, antibodies, and transgenic mice, generated for its phenotyping pipeline. The resources are freely-available to interested researchers.

Proper citation: Genes to Cognition: Neuroscience Research Programme (RRID:SCR_007121) Copy   

•   Source: SciCrunch Registry

http://rfam.xfam.org/

The Rfam database is a collection of RNA families, each represented by multiple sequence alignments, consensus secondary structures and covariance models (CMs). The families in Rfam break down into three broad functional classes: Non-coding RNA genes, structured cis-regulatory elements and self-splicing RNAs. Typically these functional RNAs often have a conserved secondary structure which may be better preserved than the RNA sequence. The CMs used to describe each family are a slightly more complicated relative of the profile hidden Markov models (HMMs) used by Pfam. CMs can simultaneously model RNA sequence and the structure in an elegant and accurate fashion. Rfam is also available via FTP. You can find data in Rfam in various ways... * Analyze your RNA sequence for Rfam matches * View Rfam family annotation and alignments * View Rfam clan details * Query Rfam by keywords * Fetch families or sequences by NCBI taxonomy * Enter any type of accession or ID to jump to the page for a Rfam family, sequence or genome

Proper citation: Rfam (RRID:SCR_007891) Copy   

•   Source: SciCrunch Registry

http://www.sanger.ac.uk/Projects/Microbes/

This website includes a list of projects that the Sanger Institute is currently working on or completed. All projects consist of the genomic sequencing of different bacteria. Each description of the bacteria includes its classification, a description, and the types of diseases that the bacteria is likely to cause. The Sanger Institute bacterial sequencing effort is concentrated on pathogens and model organisms. Data is accessible in a number of ways; for each organism there is a BLAST server, allowing users to search the sequences with their own query and retrieve the matching contigs. Sequences can also be downloaded directly by FTP. Data is accessible in a number of ways; for each organism there is a BLAST server, allowing you to search the sequences with your own query and retrieve the matching contigs. Sequences can also be downloaded directly by FTP. The primary sequence viewer and annotation tool, Artemis is available for download. This is a portable Java program which is used extensively within the Microbial Genomes group for the analysis and annotation of sequence data from cosmids to whole genomes. The Artemis Comparison Tool (ACT) is also useful for interactive viewing of the comparisons between large and small sequences.

Proper citation: Bacterial Genomes (RRID:SCR_008141) Copy   

•   Source: SciCrunch Registry

http://vega.sanger.ac.uk/

Central repository for high quality frequently updated manual annotation of vertebrate finished genome sequence. Human, mouse and zebrafish are in the process of being completely annotated, whereas for other species the annotation is only of specific genomic regions of particular biological interest. The majority of the annotation is from the HAVANA group at the Welcome Trust Sanger Institute. Users can BLAST, search for specific text, export, and download data. Genomes and details of the projects for each species are available through the homepages for human mouse and zebrafish. The website is built upon code from the EnsEMBL (http://www.ensembl.org) project. Some Ensembl features are not available in Vega. From the users point of view perhaps the most significant of these is MartView. However due to their inclusion in Ensembl, Vega human and mouse data can be queried using Ensembl MartView. Vega contains annotation of the human MHC region in eight haplotypes, and the LRC region in three haplotypes. Vega also contains annotation on the Insulin Dependent Diabetes (IDD) regions on non-reference assemblies for mouse.

Proper citation: VEGA (RRID:SCR_007907) Copy   

•   Source: SciCrunch Registry

http://www.basisproject.eu/

Consortium to generate complete catalogs of somatic mutations in 500 breast cancers, of the ER+ve HER2- subclass, under the International Cancer Genome Consortium model by high coverage, shotgun genome sequencing of both tumor and normal DNA. The strategy is to collect, store, review, quality control and extract DNA and RNA from breast cancer and normal tissues from 500 ER+, HER2- breast cancer cases which will be subjected to a coordinated series of genomic analyses including whole genome shotgun sequencing, genome-wide copy number analysis, mRNA expression analysis, miRNA expression analysis and genome-wide methylation analysis. A comprehensive catalogue of somatic mutations will be generated from each cancer. Somatic mutation catalogues from the 500 cancers will be analysed and integrated with expression and methylation data to identify novel cancer genes, characterize subverted biological pathways that are operative, describe patterns of somatic mutation and explore early translational applications of personalized somatic genomic data for patients with ER+, HER2- breast cancer. The results will impact the understanding of the causes and biology of breast cancer and will lead to major advances in detection, prevention and treatment in one of the most common diseases and causes of death in the developed world. The Consortium has completed a number of investigative exercises into the experimental protocols and technological practices relating to whole genome sequencing, epigenetics and transcriptomics including: * Completion of extensive testing of current RNA-seq protocol. * Designed and implemented a new, improved RNA-seq protocol which utilizes RNA samples regardless of their RNA Integrity Number. * Completed pilot testing of the Infinium 450k array and associated bi-sulfite sequencing. * Refined the whole genome sequencing library production protocols to produce more robust libraries. * Improved the primary variant-calling algorithms (for substitutions, insertions / deletions and rearrangements) * Developed new analytical algorithms to explore the resulting high-quality variants. As such, variant calling of whole genome sequencing data and secondary downstream analysis can begin in earnest in a trackable and automated fashion.

Proper citation: Breast Cancer Somatic Genetics Study (RRID:SCR_003832) Copy   

•   Source: SciCrunch Registry

http://www.ddduk.org/

The Deciphering Developmental Disorders (DDD) study aims to find out if using new genetic technologies can help doctors understand why patients get developmental disorders. To do this we have brought together doctors in the 23 NHS Regional Genetics Services throughout the UK and scientists at the Wellcome Trust Sanger Institute, a charitably funded research institute which played a world-leading role in sequencing (reading) the human genome. The DDD study involves experts in clinical, molecular and statistical genetics, as well as ethics and social science. It has a Scientific Advisory Board consisting of scientists, doctors, a lawyer and patient representative, and has received National ethical approval in the UK. Over the next few years, we are aiming to collect DNA and clinical information from 12,000 undiagnosed children in the UK with developmental disorders and their parents. The results of the DDD study will provide a unique, online catalogue of genetic changes linked to clinical features that will enable clinicians to diagnose developmental disorders. Furthermore, the study will enable the design of more efficient and cheaper diagnostic assays for relevant genetic testing to be offered to all such patients in the UK and so transform clinical practice for children with developmental disorders. Over time, the work will also improve understanding of how genetic changes cause developmental disorders and why the severity of the disease varies in individuals. The Sanger Institute will contribute to the DDD study by performing genetic analysis of DNA samples from patients with developmental disorders, and their parents, recruited into the study through the Regional Genetics Services. Using microarray technology and the latest DNA sequencing methods, research teams will probe genetic information to identify mutations (DNA errors or rearrangements) and establish if these mutations play a role in the developmental disorders observed in patients. The DDD initiative grew out of the groundbreaking DECIPHER database, a global partnership of clinical genetics centres set up in 2004, which allows researchers and clinicians to share clinical and genomic data from patients worldwide. The DDD study aims to transform the power of DECIPHER as a diagnostic tool for use by clinicians. As well as improving patient care, the DDD team will empower researchers in the field by making the data generated securely available to other research teams around the world. By assembling a solid resource of high-quality, high-resolution and consistent genomic data, the leaders of the DDD study hope to extend the reach of DECIPHER across a broader spectrum of disorders than is currently possible.

Proper citation: Deciphering Developmental Disorders (RRID:SCR_006171) Copy   

•   Source: SciCrunch Registry

http://www.sanger.ac.uk/resources/software/alfresco/

The aim is to develop a new visualization tool that allows effective comparative genome sequence analysis. The program will compare multiple sequences from putitatively homologous regions in different species. Results from various different existing analysis programs, such as gene prediction, protein homology and regulatory sequence prediction programs shall be visualized and used to find corresponding sequence domains. The program functions as an stand-alone application and also over the World Wide Web. With this in mind it is being developed using the Java programming language. A key feature of the program is to use available analysis programs relevant to comparative genome sequence analysis, combine the results of these, and graphically present them in an intuitive way, thereby facilitating the analysis of large genomic regions. We''ve decided to call this program Alfresco. We originally wanted to call it Fresco (FRont-End for Sequence COmparison) but that name was already taken. To run Alfresco you need to have jdk1.1 installed. Alfresco has only been tested on Solaris 2.5, Dec OSF 4.0D and Linux, but should run on any machine with jdk1.1. New: Alfresco now runs on Mac and Windows as well.

Proper citation: Alfresco - FRont-End for Sequence COmparison (RRID:SCR_010544) Copy   

•   Source: SciCrunch Registry

http://www.sanger.ac.uk/science/tools/seqtools

Software for multiple sequence alignment viewing, editing and phylogeny. It includes a set of user-configurable modes to color residues used to create high-quality reference alignments.

Proper citation: Belvu (RRID:SCR_015989) Copy   

•   Source: SciCrunch Registry

https://github.com/sanger-pathogens/Bio-Tradis

Analysis software for the output from TraDIS (Transposon Directed Insertion Sequencing) analyses of dense transposon mutant libraries. The Bio-Tradis analysis pipeline is implemented as an extensible Perl library which can either be used as is, or as a basis for the development of more advanced analysis tools.

Proper citation: Bio-tradis (RRID:SCR_015993) Copy   

•   Source: SciCrunch Registry

https://sanger-pathogens.github.io/gubbins/

Software application as an algorithm that iteratively identifies loci containing elevated densities of base substitutions while concurrently constructing a phylogeny based on the putative point mutations outside of these regions. It is used for phylogenetic analysis of genome sequences and generating highly accurate reconstructions under realistic models of short-term bacterial evolution., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Gubbins (RRID:SCR_016131) Copy   

•   Source: SciCrunch Registry

http://www.sanger.ac.uk/science/tools/seqtools

Software for sequence alignment that is a graphical dot-matrix program for detailed comparison of two sequences.

Proper citation: Dotter (RRID:SCR_016080) Copy   

•   Source: SciCrunch Registry

https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate

Software package for sequence alignment of pairwise sequence comparison. Exonerate can be used to align sequences using many alignment models, exhaustive dynamic programming, or a variety of heuristics., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Exonerate (RRID:SCR_016088) Copy   

•   Source: SciCrunch Registry

http://htslib.org/

Original SAMTOOLS package has been split into three separate repositories including Samtools, BCFtools and HTSlib. Samtools for manipulating next generation sequencing data used for reading, writing, editing, indexing,viewing nucleotide alignments in SAM,BAM,CRAM format. BCFtools used for reading, writing BCF2,VCF, gVCF files and calling, filtering, summarising SNP and short indel sequence variants. HTSlib used for reading, writing high throughput sequencing data.

Proper citation: SAMTOOLS (RRID:SCR_002105) Copy   

•   Source: SciCrunch Registry

http://www.genedb.org/Homepage

Database of genomes at various stages of completion, from early access to partial genomes with automatic annotation through to complete genomes with extensive manual curation. Its primary goals are: 1) to provide reliable access to the latest sequence data and annotation/curation for the whole range of organisms sequenced by the Pathogen group, and 2) to develop the website and other tools to aid the community in accessing and obtaining the maximum value from these data.

Proper citation: GeneDB (RRID:SCR_002774) Copy   

•   Source: SciCrunch Registry

http://www.sanger.ac.uk/Projects/D_rerio/

Database of zebrafish genome.

Proper citation: Zebrafish Genome Project (RRID:SCR_013157) Copy   

•   Source: SciCrunch Registry