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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Integra Life Sciences Resource Report Resource Website 100+ mentions |
Integra Life Sciences (RRID:SCR_010741) | commercial organization | Commercial tissue bank for human tissues. | life science, organization, commercial, surgical instrument, neurosurgery | Commercial | grid.481865.6, nlx_97702 | https://ror.org/04t8qhn97 | SCR_010741 | Integra | 2026-09-05 06:26:45 | 385 | ||||||||
|
ALLPATHS-LG Resource Report Resource Website 100+ mentions |
ALLPATHS-LG (RRID:SCR_010742) | ALLPATHS-LG | software resource | Software tool as whole genome shotgun assembler that can generate high quality genome assemblies using short reads (~100bp) such as those produced by the new generation of sequencers. | genome assembly, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Broad Institute |
PMID:21187386 | OMICS_00007, biotools:allpaths-lg | https://bio.tools/allpaths-lg | SCR_010742 | 2026-09-05 06:26:45 | 237 | |||||||
|
Celera assembler Resource Report Resource Website 50+ mentions |
Celera assembler (RRID:SCR_010750) | Celera assembler | software resource | A de novo whole-genome shotgun (WGS) DNA sequence assembler. |
is listed by: OMICtools is related to: Canu has parent organization: SourceForge |
GNU General Public License, v2 | OMICS_00009 | SCR_010750 | 2026-09-05 06:26:45 | 59 | |||||||||
|
SOAPdenovo Resource Report Resource Website 1000+ mentions |
SOAPdenovo (RRID:SCR_010752) | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 24,2023. Software tool for de novo assembly of human genomes with massively parallel short read sequencing.Short-read assembly method that can build de novo draft assembly for human sized genomes.Software package for assembling short oligonucleotide into contigs and scaffolds., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | next generation sequencing, rna, dna, de novo, genome assembly, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:20019144 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00031, biotools:soapdenovo, SCR_014986 | https://github.com/aquaskyline/SOAPdenovo2, https://bio.tools/soapdenovo, https://sources.debian.org/src/soapdenovo/, | SCR_010752 | SOAPdenovo2 | 2026-09-05 06:26:45 | 1342 | ||||||
|
SUTTA Resource Report Resource Website |
SUTTA (RRID:SCR_010754) | SUTTA | software resource | A new De Novo DNA sequence assembler based on global search-methods in order to contain the complexity of the assembly problem. | is listed by: OMICtools | OMICS_00034 | SCR_010754 | 2026-09-05 06:26:45 | 0 | ||||||||||
|
Velvet Resource Report Resource Website 1000+ mentions |
Velvet (RRID:SCR_010755) | Velvet | data analysis software, data processing software, sequence analysis software, software application, software resource | 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. | de novo, genomic, assembly, short, read, sequencing, de Bruijn, graph, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: Velvet-SC is related to: shovill has parent organization: European Bioinformatics Institute |
EMBL | PMID:18349386 DOI:10.1101/gr.074492.107 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00038, biotools:velvet | https://www.ebi.ac.uk/~zerbino/velvet/, https://bio.tools/velvet, https://sources.debian.org/src/velvet/ | SCR_010755 | 2026-09-05 06:26:46 | 1039 | |||||
|
Atlas2 Resource Report Resource Website 10+ mentions |
Atlas2 (RRID:SCR_010756) | software resource | A next-generation sequencing suite of variant analysis tools specializing in the separation of true SNPs and insertions and deletions (indels) from sequencing and mapping errors in WECS data. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Baylor University; Texas; USA |
PMID:22239737 | biotools:atlas_suite, OMICS_00051 | https://bio.tools/atlas_suite | SCR_010756 | Atlas Suite | 2026-09-05 06:26:46 | 11 | |||||||
|
FamSeq Resource Report Resource Website |
FamSeq (RRID:SCR_010760) | FamSeq | software resource | A computational tool for calculating probability of variants in family-based sequencing data. | c++ |
is listed by: OMICtools has parent organization: University of Texas MD Anderson Cancer Center |
PMID:23426633 | OMICS_00058 | SCR_010760 | Family-Based Sequencing Program | 2026-09-05 06:26:46 | 0 | |||||||
|
Ohio Northern University; Ohio; USA Resource Report Resource Website |
Ohio Northern University; Ohio; USA (RRID:SCR_000362) | ONU | university | A public university in Ohio with land, sea and space grants that offers degree programs and research at the undergraduate and graduate level. | land, sea, space, grant, ohio, public | is parent organization of: Ohio Northern University College of Pharmacy | Wikidata:Q1683585, grid.261323.7, nlx_143792, ISNI:0000 0001 2187 1348 | https://ror.org/052963a64 | SCR_000362 | 2026-09-05 06:24:19 | 0 | ||||||||
|
riboPicker Resource Report Resource Website 1+ mentions |
riboPicker (RRID:SCR_000360) | software resource | Software to automatically identify and efficiently remove rRNA-like sequences from metatranscriptomic and metagenomic datasets. | standalone software, perl, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:22155869 | Free, Available for download, Freely available | OMICS_02618, biotools:ribopicker | https://bio.tools/ribopicker | SCR_000360 | 2026-09-05 06:24:17 | 2 | |||||||
|
ARACHNE Resource Report Resource Website 1+ mentions |
ARACHNE (RRID:SCR_000351) | ARACHNE | software resource | A software for genome assembly, and is specifically designed to analyze long Sanger-chemistry reads. | genome, sequencing, analysis, sanger, chemistry, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Broad Institute |
PMID:11779843 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01812, biotools:arachne | https://bio.tools/arachne | SCR_000351 | ARACHNE: a whole-genome shotgun assembler, ARACHNE (Unsupported) | 2026-09-05 06:24:17 | 3 | |||||
|
ParseCNV Resource Report Resource Website 1+ mentions |
ParseCNV (RRID:SCR_000355) | software resource | Software that takes CNV calls as input and creates SNP based statistics for CNV occurrence in cases and controls then calls CNVRs based on neighboring SNPs of similar significance. | standalone software |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23293001 | Free, Available for download, Freely available | OMICS_02566 | SCR_000355 | 2026-09-05 06:24:17 | 1 | ||||||||
|
Kinannote Resource Report Resource Website 1+ mentions |
Kinannote (RRID:SCR_000352) | software resource | Software that identifies and classifies protein kinases in a user-provided fasta file using an HMM derived from serine / threonine protein kinases, a position specific scoring matrix derived from the HMM, and comparison with a local version of the curated kinase database from kinase.com. | standalone software, perl |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23904509 | Free, Available for download, Freely available | OMICS_05965 | SCR_000352 | 2026-09-05 06:24:19 | 2 | ||||||||
|
HudsonAlpha Genomics Services Lab Resource Report Resource Website |
HudsonAlpha Genomics Services Lab (RRID:SCR_000353) | HudsonAlpha Genomics Services Lab | service resource | A lab that offers genetic research tools such as RNA sequencing and a variety of arrays. | genome, sequencing, assembly, rna, microarray, exome | is listed by: ScienceExchange | THIS RESOURCE IS NO LONGER IN SERVICE | SciEx_221 | SCR_000353 | HudsonAlpha Institute for Biotechnology Genomics Services Lab, Genomics Services Lab | 2026-09-05 06:24:17 | 0 | |||||||
|
Jnomics Resource Report Resource Website |
Jnomics (RRID:SCR_000348) | software resource | A collection of cloud-scale DNA sequence analysis tools. | mapreduce |
is listed by: OMICtools has parent organization: SourceForge |
Free, Available for download, Freely available | OMICS_04074 | SCR_000348 | 2026-09-05 06:24:17 | 0 | |||||||||
|
ABrowse Resource Report Resource Website 1+ mentions |
ABrowse (RRID:SCR_000345) | software resource | A genome browser framework which gives an open browsing experience, open data access, collaborative work support, and a framework to import annotations. Multiple data access approaches are supported for external platforms to retrieve data from ABrowse. This resource also contains an online user-space in which users can create, store and share comments, annotations and landmarks. | genome browser, collaborative work, open data access, collaborative work support, framework, import annotation |
is listed by: OMICtools is related to: Galaxy |
PMID:22222089 | Free, Available for download, Freely available | OMICS_00899 | SCR_000345 | 2026-09-05 06:24:17 | 4 | ||||||||
|
GPViz Resource Report Resource Website |
GPViz (RRID:SCR_000346) | GPViz | software resource | A versatile Java-based software used for dynamic gene-centered visualization of genomic regions and/or variants. | gene, visualization, genomic, variant, bioinformatics, java | is listed by: OMICtools | Free, Available for download, Freely available | OMICS_00915 | SCR_000346 | 2026-09-05 06:24:19 | 0 | ||||||||
|
TEDDY Resource Report Resource Website 1+ mentions |
TEDDY (RRID:SCR_000383) | TEDDY | clinical trial, consortium, data or information resource, database, organization portal, portal | International consortium of six centers assembled to participate in the development and implementation of studies to identify infectious agents, dietary factors, or other environmental agents, including psychosocial factors, that trigger type 1 diabetes in genetically susceptible people. The coordinating centers recruit and enroll subjects, obtaining informed consent from parents prior to or shortly after birth, genetic and other types of samples from neonates and parents, and prospectively following selected neonates throughout childhood or until development of islet autoimmunity or T1DM. The study tracks child diet, illnesses, allergies and other life experiences. A blood sample is taken from children every 3 months for 4 years. After 4 years, children will be seen every 6 months until the age of 15 years. Children are tested for 3 different autoantibodies. The study will compare the life experiences and blood and stool tests of the children who get autoantibodies and diabetes with some of those children who do not get autoantibodies or diabetes. In this way the study hopes to find the triggers of T1DM in children with higher risk genes. | consortium, gene, infectious agent, dietary factor, environmental factor, young human, insulin, child, pediatric, autoantibody, blood, stool, biomaterial supply resource, longitudinal, neonate, parent, genetic risk, genetic factor, observation, prospective, serum, plasma, peripheral blood mononuclear cell, saliva, nasal swab, nail clipping, water, dna, virus, nutrition, toxic agent, socioeconomic, psychosocial, male, female, environment, exposure, diet, toxin, infectious agent, bacterial, viral, immunization |
is listed by: One Mind Biospecimen Bank Listing is listed by: ClinicalTrials.gov is listed by: NIDDK Information Network (dkNET) is listed by: NIDDK Central Repository is related to: Teddy study IA prediction has parent organization: University of South Florida; Florida; USA |
Type 1 diabetes, Diabetes | NIDDK 2UC4DK063829 | PMID:21564455 | nlx_152857 | SCR_000383 | The Environmental Determinants of Diabetes in the Young, TEDDY study | 2026-09-05 06:24:18 | 3 | |||||
|
Trans-Institute Angiogenesis Research Program Resource Report Resource Website |
Trans-Institute Angiogenesis Research Program (RRID:SCR_000384) | TARP | data or information resource, portal, resource, topical portal | Trans-NIH program encouraging and facilitating the study of the underlying mechanisms controlling blood vessel growth and development. Other aims include: to identify specific targets and to develop therapeutics against pathologic angiogenesis in order to reduce the morbidity due to abnormal blood vessel proliferation in a variety of disease states; to better understand the process of angiogenesis and vascularization to improve states of decreased vascularization; to encourage and facilitate the study of the processes of lymphangiogenesis; and to achieve these goals through a multidisciplinary approach, bringing together investigators with varied backgrounds and varied interests. | blood vessel, growth, development, target, therapeutic, vascularization, angiogenesis, lymphangiogenesis |
is listed by: NIDDK Information Network (dkNET) has parent organization: National Institutes of Health |
Angiogenesis, Lymphangiogenesis | JDRF ; NEI ; NHLBI ; NCI ; NICHD ; NIDDK ; NINDS |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_152866 | SCR_000384 | Trans-Institute Angiogenesis Research Program (TARP) | 2026-09-05 06:24:18 | 0 | |||||
|
SunnyLab Resource Report Resource Website |
SunnyLab (RRID:SCR_000382) | commercial organization | An antibody supplier that provides a range of human antigens, serum and plasma, and cell culture reagents. | antibody, antigen, reagent, serum, plasma, culture, commercial | Commercially available | nlx_152472 | SCR_000382 | 2026-09-05 06:24:20 | 0 |
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