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http://www.molecularevolution.org/software/genomics/velvet

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software package as de novo genomic assembler for short read sequencing technologies using de Bruijn graphs. Takes in short read sequences, removes errors, then produces high quality unique contigs, retrieves repeated areas between contigs. Can leverage very short reads in combination with read pairs to produce useful assemblies. Operating system Unix/Linux., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Velvet (RRID:SCR_010755) Copy   

•   Source: SciCrunch Registry

http://homer.ucsd.edu/

Software tools for Motif Discovery and next-gen sequencing analysis. Used for analyzing ChIP-Seq, GRO-Seq, RNA-Seq, DNase-Seq, Hi-C and numerous other types of functional genomics sequencing data sets. Collection of command line programs for unix style operating systems written in Perl and C++.

Proper citation: HOMER (RRID:SCR_010881) Copy   

•   Source: SciCrunch Registry

http://tagcleaner.sourceforge.net/

A software tool which can automatically detect and efficiently remove tag sequences from genomic and metagenomic datasets.

Proper citation: TagCleaner (RRID:SCR_011846) Copy   

•   Source: SciCrunch Registry

https://www.q2labsolutions.com/genomics-laboratories

Core provides whole genome to focused set gene expression and genotyping assays along with DNA sequencings services, sequence enrichment technologies and bioinformatics support. Platforms utilized include Affymetrix GeneChip, Agilent Sure Select, Fluidigm Access Arrays, Illumina BeadChip, iScan, Genome Analyzer and Hi-Seq, RainDance Technologies RDT 1000 and, the Pacific Biosciences PacBio RS. Expression Analysis offers solutions for challenging specimens such as whole blood and FFPE tissues, as well as nucleic acid isolation and data analysis services.

Proper citation: Q Squared Solutions Expression Analysis (RRID:SCR_012497) Copy   

•   Source: SciCrunch Registry

https://code.google.com/p/ontology-for-genetic-interval/

An ontology that formalized the genomic element by defining an upper class genetic interval using BFO as its framework. The definition of genetic interval is the spatial continuous physical entity which contains ordered genomic sets (DNA, RNA, Allele, Marker,etc.) between and including two points (Nucleic_Acid_Base_Residue) on a chromosome or RNA molecule which must have a liner primary sequence structure.

Proper citation: Ontology for Genetic Interval (RRID:SCR_003423) Copy   

•   Source: SciCrunch Registry

http://ssadedin.github.io/ximmer/

Software to help users of targeted high throughput genomic sequencing data to accurately detect copy number variants (CNVs). Framework for running and evaluating other copy number detection tools.Used for evaluating and improving performance of CNV detection in exome and targeted sequencing data.

Proper citation: Ximmer (RRID:SCR_016427) Copy   

•   Source: SciCrunch Registry

https://gotrack.msl.ubc.ca/

Open source web-based system and database that provides access to historical records and trends in the Gene Ontology (GO) and GO annotations (GOA). Used for monitoring changes in the Gene Ontology and their impact on genomic data analysis.

Proper citation: GOTrack (RRID:SCR_016399) Copy   

•   Source: SciCrunch Registry

https://genome.jgi.doe.gov/programs/fungi/1000fungalgenomes.jsf

Web application to provide genomic information for fungi. Includes sequenced fungal genomes, those in progress, and selected nominations. Nomination of new species for genome sequencing in the families or only one reference genome possible after providing DNA/RNA samples for their sequencing. Used to explore the diversity of fungi important for energy and the environment.

Proper citation: 1000 Fungal Genome Project (RRID:SCR_016463) Copy   

•   Source: SciCrunch Registry

http://gcm.wfcc.info/

Database and information retrieval, analysis, and visualization system for microbial resources to help culture collections to manage, disseminate and share the information related to their holdings. Provides an interface for the scientific and industrial communities to access the microbial resource information.

Proper citation: Global Catalogue of Microorganisms (RRID:SCR_016460) Copy   

•   Source: SciCrunch Registry

http://cajadb.neuro.ufrn.br

Software application as an integrated web resource of marmoset biological data. Used to find genomic, expression and alternative splicing data to facilitate the study of animal model for neuropsychiatric and social behavior research and to support biological analyses such as functional (ontology) enrichment analysis and protein-protein-network.

Proper citation: CajaDB (RRID:SCR_016506) Copy   

•   Source: SciCrunch Registry

https://pave.niaid.nih.gov

Collection of curated papillomavirus genomic sequences, accompanied by web-based sequence analysis tools. Database and web applications support the storage, annotation, analysis, and exchange of information.

Proper citation: PaVE (RRID:SCR_016599) Copy   

•   Source: SciCrunch Registry

https://github.com/INTABiotechMJ/MITE-Tracker

Open source software tool for identifying miniature inverted repeat transposable elements in large genomes. Used to process large scale genomes, to find and classify MITEs using an efficient alignment strategy to retrieve nearby inverted repeat sequences.

Proper citation: MITE-Tracker (RRID:SCR_017030) Copy   

•   Source: SciCrunch Registry

http://www.imperial.ac.uk/research/animallectins

Resource presents information about animal lectins involved in various sugar recognition processes.

Proper citation: genomics resource for animal lectins (RRID:SCR_018122) Copy   

•   Source: SciCrunch Registry

https://bioservices.uncc.edu

Core to assist with analyzing and interpreting data produced by genomic technologies.

Proper citation: University of North Carolina Charlotte Bioinformatics Services Division (RRID:SCR_017182) Copy   

•   Source: SciCrunch Registry

https://www.cityofhope.org/research/shared-resources/integrative-genomics-and-bioinformatics

Core provides genomic and bioinformatics services to City of Hope Comprehensive Cancer Center (COHCCC) investigators.

Proper citation: City of Hope National Medical Center Integrative Genomics and Bioinformatics Core Facility (RRID:SCR_017188) Copy   

•   Source: SciCrunch Registry

https://github.com/ZSI-Bio/bdg-sequila

Software tool for genomic intervals querying and processing built on top of Apache Spark. Elastic, fast and scalable SQL oriented solution for processing and querying genomic intervals.

Proper citation: SeQuiLa (RRID:SCR_017220) Copy   

•   Source: SciCrunch Registry

https://www.bmh.manchester.ac.uk/research/facilities/bioinformatics/

Core provides assistance in integrative analysis of genomic datasets to support faculty.

Proper citation: University of Manchester Bioinformatics Core Facility (RRID:SCR_017171) Copy   

•   Source: SciCrunch Registry

https://glomcon.org

Consortium to bring together clinicians, pathologists, researchers, and biotech innovators to create scalable network of stakeholders interested in helping patients with glomerular kidney disease. Makes collective expertise of its members available for discussion of individual cases, provides infrastructure for biomarker studies, enables genomic research, and facilitates clinical trials.

Proper citation: Glomerular Disease Study & Trial Consortium (RRID:SCR_017264) Copy   

•   Source: SciCrunch Registry

https://anvilproject.org/

Portal to facilitate integration and computing on and across large datasets generated by NHGRI programs, as well as initiatives funded by National Institutes of Health or by other agencies that support human genomics research. Resource for genomic scientific community, that leverages cloud based infrastructure for democratizing genomic data access, sharing and computing across large genomic, and genomic related data sets. Component of federated data ecosystem, and is expected to collaborate and integrate with other genomic data resources through adoption of FAIR (Findable, Accessible, Interoperable, Reusable) principles, as their specifications emerge from scientific community. Will provide collaborative environment, where datasets and analysis workflows can be shared within consortium and be prepared for public release to broad scientific community through AnVIL user interfaces.

Proper citation: Analysis, Visualization, and Informatics Lab-space (AnVIL) (RRID:SCR_017469) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/TCGAbiolinks/

Software R Bioconductor package for integrative analysis with TCGA data.TCGAbiolinks is able to access National Cancer Institute Genomic Data Commons thorough its GDC Application Programming Interface to search, download and prepare relevant data for analysis in R.

Proper citation: TCGAbiolinks (RRID:SCR_017683) Copy   

•   Source: SciCrunch Registry