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http://genome.jgi.doe.gov/programs/fungi/index.jsf

Fungal genomics database and interactive analytical tools that integrates all fungal genomes for diverse fungi that are important for energy and environment, the focus of the JGI Fungal program. It integrates genomics data from the DOE JGI and its users and promotes user community participation in data submission, annotation and analysis. Over 100 newly sequenced and annotated fungal genomes from JGI and elsewhere are available to the public through MycoCosm, and new annotated genomes are being added to this resource upon completion of annotation. MycoCosm offers web-based genome analysis tools for fungal biologists to ''navigate'' through sequenced genomes and explore them in the context of ''genome-centric'' and ''comparative views''.

Proper citation: MycoCosm (RRID:SCR_005312) Copy   

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http://last.cbrc.jp/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software tool for aligning sequences, similar to BLAST 2 sequences that colour-codes the alignments by reliability. Another useful feature of LAST is that it can compare huge (vertebrate-genome-sized) datasets. Unfortunately, this only applies to the downloadable version of LAST, not the web service. The web service can just about handle bacterial genomes, but it will take a few minutes and the output will be large. LAST can: * Handle big sequence data, e.g: ** Compare two vertebrate genomes ** Align billions of DNA reads to a genome * Indicate the reliability of each aligned column. * Use sequence quality data properly. * Compare DNA to proteins, with frameshifts. * Compare PSSMs to sequences * Calculate the likelihood of chance similarities between random sequences. LAST cannot (yet): * Do spliced alignment., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: LAST (RRID:SCR_006119) Copy   

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https://www.facebase.org/

A web portal that provides access to data, tools and materials that will aid in craniofacial research. Included is access to genomic and imaging based data sets from a variety of species, including zebrafish, human and mouse.

Proper citation: FaceBase (RRID:SCR_005998) Copy   

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https://www.iscaconsortium.org/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 22, 2022. A rapidly growing group of clinical cytogenetics and molecular genetics laboratories committed to improving quality of patient care related to clinical genetic testing using new molecular cytogenetic technologies including array comparative genomic hybridization (aCGH) and quantitative SNP analysis by microarrays or bead chip technology. They improve clinical care by providing a large publicly available database and forum where clinicians and researchers can share knowledge to expedite the understanding of copy number variation (CNV) in an abnormal population. The ISCA database contains whole genome array data from a subset of the ISCA Consortium clinical diagnostic laboratories. Array analysis was carried out on individuals with phenotypes including intellectual disability, autism, and developmental delay. Efforts of the Consortium include: # Clinical Utility: The ISCA Consortium has made recommendations regarding the appropriate clinical indications for cytogenetic array testing (Miller et al. AJHG 2010, PMID: 20466091). Currently, discussions are focused on pediatric applications for children with unexplained developmental delay, intellectual disability, autism and other developmental disabilities. A separate committee has been developed to address appropriate cancer genetic applications (http://www.urmc.rochester.edu/ccmc/). # Evidence-based standards for cytogenomic array design: The Consortium will develop recommendations for standards for the design, resolution and content of cytogenomic arrays using an evidence-based process and an international panel of experts in clinical genetics, clinical laboratory genetics (cytogenetics and molecular genetics), genomics and bioinformatics. This design is intended to be platform and vendor-neutral (common denominator is genome sequence coordinates), and is a dynamic process with input from the broader genetics community and evidence-based review by the expert panel (which will evolve into a Standing Committee with international representation). # Public Database for clinical and research community: It is essential that publicly available databases be created and maintained for cytogenetic array data generated in clinical testing laboratories. The ISCA data will be held in dbGaP and dbVar at NCBI/NIH and curated by a committee of clinical genetics laboratory experts. The very high quality of copy number data (i.e., deletions and duplications) coming from clinical laboratories combined with expert curation will produce an invaluable resource to the clinical and research communities. # Standards for interpretation of cytogenetic array results: Using the ISCA Database, along with other genomic and genetics databases, the Consortium will develop recommendations for the interpretation and reporting of pathogenic vs. benign copy number changes as well as imbalances of unknown clinical significance.

Proper citation: ISCA Consortium (RRID:SCR_006168) Copy   

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https://www.synapse.org/

A cloud-based collaborative platform which co-locates data, code, and computing resources for analyzing genome-scale data and seamlessly integrates these services allowing scientists to share and analyze data together. Synapse consists of a web portal integrated with the R/Bioconductor statistical package and will be integrated with additional tools. The web portal is organized around the concept of a Project which is an environment where you can interact, share data, and analysis methods with a specific group of users or broadly across open collaborations. Projects provide an organizational structure to interact with data, code and analyses, and to track data provenance. A project can be created by anyone with a Synapse account and can be shared among all Synapse users or restricted to a specific team. Public data projects include the Synapse Commons Repository (SCR) (syn150935) and the metaGenomics project (syn275039). The SCR provides access to raw data and phenotypic information for publicly available genomic data sets, such as GEO and TCGA. The metaGenomics project provides standardized preprocessed data and precomputed analysis of the public SCR data.

Proper citation: Synapse (RRID:SCR_006307) Copy   

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http://coot.embl.de/g2d/

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. A database of candidate genes for mapped inherited human diseases. Candidate priorities are automatically established by a data mining algorithm that extracts putative genes in the chromosomal region where the disease is mapped, and evaluates their possible relation to the disease based on the phenotype of the disorder. Data analysis uses a scoring system developed for the possible functional relations of human genes to genetically inherited diseases that have been mapped onto chromosomal regions without assignment of a particular gene. Methodology can be divided in two parts: the association of genes to phenotypic features, and the identification of candidate genes on a chromosonal region by homology. This is an analysis of relations between phenotypic features and chemical objects, and from chemical objects to protein function terms, based on the whole MEDLINE and RefSeq databases.

Proper citation: Candidate Genes to Inherited Diseases (RRID:SCR_008190) Copy   

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http://www.genome.arizona.edu/

Their primary focus is in the area of structural, evolutionary and functional genomics of crop plants. AGI is divided into 5 Centers each lead by a Center Leader and a senior Manager (BAC Library Construction Center, BAC/EST Resource Center, Sequencing & Physical Mapping Center (including: production sequencing and fingerprinting, and sequence finishing), Bioinformatics Center and the Evolutionary and Functional Genomics Center). AGI is housed in the state of the art Thomas W. Keating Bioresearch Building on the northeast part of campus near the Medical School. AGI currently employees about 30 scientists and is primarily funded through federal grants, private contracts, and the Bud Antle Endowed Chair in Plant Molecular Genetics. Sponsors: AGI is supported by Bio5, Plant Sciences, National Science Foundation, National Institues oh Health, and USDA.

Proper citation: AGI (RRID:SCR_007203) Copy   

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http://genes.toronto.edu/

The Frey Lab develops techniques that use large scale datasets to derive predictive models of how genes and many other genomic features act in combination to produce genetic messages that control cellular activities. We have most recently focused on how organisms use alternative splicing to generate a tremendous level of biological complexity that cannot be explained by gene expression alone (Nature, 2010). Some of the tools, software and databases provided by the Frey Lab are affinity propagation, splicing prediction, PTMClust - A Post-translational Modification Refinement Algorithm, the ''epitome'': A new model of patterns, transformation invariant clustering and subspaces, learning flexible sprites from images and videos, phase unwrapping by loopy belief propagation, useful Matlab scripts, bioinformatics links, and SeedSearcher: A motif finder.

Proper citation: Frey Lab (RRID:SCR_008859) Copy   

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http://bioinf.wehi.edu.au/software/linkdatagen

Perl tool that generates linkage mapping input files using data from HAPMAP Phase III populations. It provides rudimentary error checks and is easily amended for personal linkage mapping preferences.

Proper citation: LINKDATAGEN (RRID:SCR_015625) Copy   

•   Source: SciCrunch Registry

https://github.com/HingeAssembler/HINGE

Software application for long read genome assembly based on hinging. Used in long-read sequencing technologies in genome assemblies to achieve optimal repeat resolution.

Proper citation: Hinge (RRID:SCR_016135) Copy   

•   Source: SciCrunch Registry

http://jjwanglab.org/gwasrap

GWASrap is a comprehensive web-based bioinformatics tool to systematically support variant representation, annotation and prioritization for data generated from genome-wide association studies (GWAS) and Next Generation Sequencing (NGS). Our web-based framework utilizes state-of-the-art web technologies to maximize user interaction and visualization of the results. For a given SNP dataset with its P-values, GWASrap will first provide a Circos-style plot to visualize any genetic variants at either the genome or chromosome level. The tool then combines different genomic features (SNP/CNV density, disease susceptibility loci, etc.) with comprehensive annotations that give the researcher an intuitive view of the functional significance of the different genomic regions. The detailed statistics of the underlying study are also displayed on the web page, including variant distribution in different functional categories, classic Manhattan plot and QQ plot. Users can perform interactive operations in the Manhattan panel, such as zooming in and out to search regions or markers of interest. The system can also display a comprehensive range of relevant information from variant genetic attributes to nearby genomic elements, such as enhancers or non-coding RNAs. Furthermore, researchers can obtain extensive functional predictions for various features including transcription factor-binding sites, miRNA and miRNA target sites, and their predicted changes caused by the genetic variants. Our system can re-prioritize genetic variants by combining the original statistical value and variant prioritization score based on a simple additive effect equation. Researchers can also re-evaluate the significance of a trait/disease-associated SNP (TAS) using the dynamic linkage disequilibrium (LD) panel or the tree-like network panel. The GWASrap supports input variants in different formats, not only common variants with a dbSNP rs ID but also rare variants from NGS data, which are represented by chromosome and locations. GWASrap provides a range of web services for data retrieving about the annotation information and effect prediction of each variant in dbSNP using the SOAP interface. The WSDL for each service is available in the API tab. Each service returns JSON string including all related information with key/value. GWASrap provides running results about some current published GWAS as well as a category view for each hot disease / trait. The dataset is brought from published database GWAS or curated from literature.

Proper citation: GWASrap (RRID:SCR_013144) Copy   

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https://github.com/broadinstitute/pilon/

Software tool to automatically improve draft assemblies and find variation among strains, including large event detection. FASTA files of genome along with one or more BAM files of reads aligned as input. Read alignment analysis is used to identify inconsistencies between input genome and evidence in reads, then attempts to make improvements to genome.

Proper citation: Pilon (RRID:SCR_014731) Copy   

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https://github.com/xavierdidelot/clonalorigin

Software package for comparative analysis of the sequences of a sample of bacterial genomes in order to reconstruct the recombination events that have taken place in their ancestry.

Proper citation: ClonalOrigin (RRID:SCR_016061) Copy   

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https://chlorobox.mpimp-golm.mpg.de/OGDraw.html

Software package for graphical visualization of organellar genomes. Converts annotations in GenBank format into graphical maps. Used to create visual representations of circular and linear annotated genome sequences provided as GenBank files or accession numbers.

Proper citation: OGDraw (RRID:SCR_017337) Copy   

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https://broadinstitute.github.io/warp/docs/Pipelines/Optimus_Pipeline/README

Optimus is a pipeline developed by the Data Coordination Platform (DCP) of the Human Cell Atlas (HCA) Project that supports processing of any 3' single-cell and single-nuclei expression data generated with the 10x Genomic v2 or v3 assay. It is an alignment and transcriptome quantification pipeline that corrects cell barcodes, aligns reads to the genome, corrects Unique Molecular Identifiers (UMIs), generates an expression matrix in a UMI-aware manner, calculates summary metrics for genes and cells, detects empty droplets, returns read outputs in BAM format, and returns gene counts in NumPy matrix and Loom matrix formats.

Proper citation: Optimus Pipeline (RRID:SCR_018908) Copy   

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http://www.cazy.org

Database that describes the families of structurally-related catalytic and carbohydrate-binding modules (or functional domains) of enzymes that degrade, modify, or create glycosidic bonds. This specialist database is dedicated to the display and analysis of genomic, structural and biochemical information on Carbohydrate-Active Enzymes (CAZymes). CAZy data are accessible either by browsing sequence-based families or by browsing the content of genomes in carbohydrate-active enzymes. New genomes are added regularly shortly after they appear in the daily releases of GenBank. New families are created based on published evidence for the activity of at least one member of the family and all families are regularly updated, both in content and in description. An original aspect of the CAZy database is its attempt to cover all carbohydrate-active enzymes across organisms and across subfields of glycosciences. One can search for CAZY Family pages using the Protein Accession (Genpept Accession, Uniprot Accession or PDB ID), Cazy family name or EC number. In addition, genomes can be searched using the NCBI TaxID. This search can be complemented by Google-based searches on the CAZy site.

Proper citation: CAZy- Carbohydrate Active Enzyme (RRID:SCR_012909) Copy   

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http://www.cdc.gov/genomics/hugenet/default.htm

Human Genome Epidemiology Network, or HuGENet, is a global collaboration of individuals and organizations committed to the assessment of the impact of human genome variation on population health and how genetic information can be used to improve health and prevent disease. Its goals include: establishing an information exchange that promotes global collaboration in developing peer-reviewed information on the relationship between human genomic variation and health and on the quality of genetic tests for screening and prevention; providing training and technical assistance to researchers and practitioners interested in assessing the role of human genomic variation on population health and how such information can be used in practice; developing an updated and accessible knowledge base on the World Wide Web; and promoting the use of this knowledge base by health care providers, researchers, industry, government, and the public for making decisions involving the use of genetic information for disease prevention and health promotion. HuGENet collaborators come from multiple disciplines such as epidemiology, genetics, clinical medicine, policy, public health, education, and biomedical sciences. Currently, there are 4 HuGENet Coordinating Centers for the implementation of HuGENet activities: CDC''s Office of Public Health Genomics, Atlanta, Georgia; HuGENet UK Coordinating Center, Cambridge, UK; University of Ioannina, Greece; University of Ottawa , Ottawa, Canada. HuGENet includes: HuGE e-Journal Club: The HuGE e-Journal Club is an electronic discussion forum where new human genome epidemiologic (HuGE) findings, published in the scientific literature in the CDC''s Office of Public Health Genomics Weekly Update, will be abstracted, summarized, presented, and discussed via a newly created HuGENet listserv. HuGE Reviews: A HuGE Review identifies human genetic variations at one or more loci, and describes what is known about the frequency of these variants in different populations, identifies diseases that these variants are associated with and summarizes the magnitude of risks and associated risk factors, and evaluates associated genetic tests. Reviews point to gaps in existing epidemiologic and clinical knowledge, thus stimulating further research in these areas. HuGE Fact Sheets: HuGE Fact Sheets summarize information about a particular gene, its variants, and associated diseases. HuGE Case Studies: An on-line presentation designed to sharpen your epidemiological skills and enhance your knowledge on genomic variation and human diseases. Its purpose is to train health professionals in the practical application of human genome epidemiology (HuGE), which translates gene discoveries to disease prevention by integrating population-based data on gene-disease relationships and interventions. Students will acquire conceptual and practical tools for critically evaluating the growing scientific literature in specific disease areas. HUGENet Publications: Articles related to the HuGENet movement written by our HuGENet collaborators. HuGE Navigator: An integrated, searchable knowledge base of genetic associations and human genome epidemiology, including information on population prevalence of genetic variants, gene-disease associations, gene-gene and gene- environment interactions, and evaluation of genetic tests. HuGE Workshops: HuGENet has sponsored meetings and workshops with national and international partners since 2001. Available are detailed summaries, agendas or the ability to download speaker slides. HuGE Book: Human Genome Epidemiology: A Scientific Foundation for Using Genetic Information to Improve Health and Prevent Disease. (The findings and conclusions in this book are those of the author(s) and do not necessarily represent the views of the funding agency.) HuGENet Collaborators: HuGENet is interested in establishing collaborations with individuals and organizations working on population based research involving genetic information. HuGE Funding: Funding opportunities for specific population-based genetic epidemiology research projects are available. Research initiatives whose aims include assessing the prevalence of human genetic variation, the association between genetic variants and human diseases, the measurement of gene-gene or gene-environment interaction, and the evaluation of genetic tests for screening and prevention are compiled to create a posted listing. Additional information and application details can be found by clicking on the respective links.

Proper citation: Human Genome Epidemiology Network (RRID:SCR_013117) Copy   

•   Source: SciCrunch Registry

http://david.abcc.ncifcrf.gov/content.jsp?file=/ease/ease1.htm&type=1

Windows(c) desktop software application, customizable and standalone, that facilitates the biological interpretation of gene lists derived from the results of microarray, proteomic, and SAGE experiments. Provides statistical methods for discovering enriched biological themes within gene lists, generates gene annotation tables, and enables automated linking to online analysis tools. Offers statistical models to deal with multi-test comparison problem. Platform: Windows compatible

Proper citation: EASE: the Expression Analysis Systematic Explorer (RRID:SCR_013361) Copy   

•   Source: SciCrunch Registry

Ratings or validation data are available for this resource

https://www.gencodegenes.org

Human and mouse genome annotation project which aims to identify all gene features in the human genome using computational analysis, manual annotation, and experimental validation.

Proper citation: GENCODE (RRID:SCR_014966) Copy   

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https://www.ncbi.nlm.nih.gov/genbank/wgs/

Project for assemblies of incomplete genomes or incomplete chromosomes of prokaryotes or eukaryotes that are being sequenced by a whole genome shotgun strategy. WGS projects may be annotated, but annotation is not required. The nucleotide and protein data from all WGS projects go into the BLAST database.

Proper citation: Whole Genome Shotgun (WGS) Project (RRID:SCR_016637) Copy   

•   Source: SciCrunch Registry