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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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cortex var Resource Report Resource Website 1+ mentions |
cortex var (RRID:SCR_005081) | cortex_var | software resource | A tool for genome assembly and variation analysis from sequence data. You can use it to discover and genotype variants on single or multiple haploid or diploid samples. If you have multiple samples, you can use Cortex to look specifically for variants that distinguish one set of samples (eg phenotype=X, cases, parents, tumour) from another set of samples (eg phenotype=Y, controls, child, normal). cortex_var features * Variant discovery by de novo assembly - no reference genome required * Supports multicoloured de Bruijn graphs - have multiple samples loaded into the same graph in different colours, and find variants that distinguish them. * Capable of calling SNPs, indels, inversions, complex variants, small haplotypes * Extremely accurate variant calling - see our paper for base-pair-resolution validation of entire alleles (rather than just breakpoints) of SNPs, indels and complex variants by comparison with fully sequenced (and finished) fosmids - a level of validation beyond that demanded of any other variant caller we are aware of - currently cortex_var is the most accurate variant caller for indels and complex variants. * Capable of aligning a reference genome to a graph and using that to call variants * Support for comparing cases/controls or phenotyped strains * Typical memory use: 1 high coverage human in under 80Gb of RAM, 1000 yeasts in under 64Gb RAM, 10 humans in under 256 Gb RAM | genome assembly, variation analysis, sequence, variation, genotype variant, haploid, diploid, snp, indel, inversion, variant, haplotype, de novo assembly, genotyping, variant-calling, population analysis, population assembly |
is listed by: OMICtools has parent organization: SourceForge has parent organization: Wellcome Trust Centre for Human Genetics |
PMID:22231483 | GNU General Public License, v3, Acknowledgement requested | OMICS_00056 | SCR_005081 | cortex_var - for variant and population assembly | 2026-02-14 02:01:03 | 3 | ||||||
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Applied Biosystems Resource Report Resource Website 10000+ mentions |
Applied Biosystems (RRID:SCR_005039) | commercial organization | An Antibody supplier | is parent organization of: Ambion Inc. | nlx_152278 | SCR_005039 | 2026-02-14 02:01:03 | 32510 | |||||||||||
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SOPRA Resource Report Resource Website 10+ mentions |
SOPRA (RRID:SCR_005035) | SOPRA | software resource | Software tool to exploit the mate pair/paired-end information for assembly of short reads from high throughput sequencing platforms, e.g. Illumina and SOLiD. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Rutgers University; New Jersey; USA |
PMID:20576136 | Acknowledgement requested | biotools:sopra, OMICS_00049 | https://bio.tools/sopra | SCR_005035 | SOPRA - Statistical Optimization of Paired Read Assembly, Statistical Optimization of Paired Read Assembly | 2026-02-14 02:00:48 | 20 | |||||
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Bioworld Technology Resource Report Resource Website 1+ mentions |
Bioworld Technology (RRID:SCR_005036) | commercial organization | An Antibody supplier | nlx_152317 | SCR_005036 | 2026-02-14 02:01:02 | 1 | ||||||||||||
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Gift of Hope Organ and Tissue Donor Network Resource Report Resource Website |
Gift of Hope Organ and Tissue Donor Network (RRID:SCR_004968) | Gift of Hope | nonprofit organization | Gift of Hope Organ & Tissue Donor Network is proud to serve as the federally designated not-for-profit agency that coordinates organ and tissue donation and supports families of donors in the northern three-quarters of Illinois and northwest Indiana. Since our inception in 1986, we have coordinated donations that have saved the lives of 17,000 organ transplant recipients and helped hundreds of thousands of other patients receive needed tissue transplants. As one of 58 organ procurement organizations (OPOs) that make up the nation''s organ donation system, we work with 179 hospitals in our donation service area. In managing the recovery, care and transportation of donated organs to transplant patients, we work closely with Illinois'' nine transplant centers, which operate 32 transplant programs. We also work with other transplant centers and other OPOs through the United Network for Organ Sharing (UNOS) to provide lifesaving organs for patients awaiting them. UNOS is the federally mandated registration center for organ transplant candidates in the United States. UNOS'' computer-based system matches donated organs with patients in need, in accordance with strict federal guidelines intended to ensure equitable distribution. | is listed by: One Mind Biospecimen Bank Listing | grid.477192.e, nlx_93206, ISNI: 0000 0004 0628 5713 | https://ror.org/00swcah48 | SCR_004968 | Gift of Hope Organ & Tissue Donor Network | 2026-02-14 02:01:01 | 0 | ||||||||
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SSPACE Resource Report Resource Website 100+ mentions |
SSPACE (RRID:SCR_005056) | SSPACE | software resource | A stand-alone software program for scaffolding pre-assembled contigs using paired-read data. Main features are: a short runtime, multiple library input of paired-end and/or mate pair datasets and possible contig extension with unmapped sequence reads. | scaffolding, contig, genome, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:21149342 DOI:10.1093/bioinformatics/btq683 |
GNU General Public License, Registration required | biotools:sspace, OMICS_00050 | https://bio.tools/sspace https://sources.debian.org/src/sspace/ |
SCR_005056 | 2026-02-14 02:01:02 | 426 | ||||||
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HPC-CLUST Resource Report Resource Website 1+ mentions |
HPC-CLUST (RRID:SCR_005052) | HPC-CLUST | software resource | A set of tools designed to cluster large numbers (>1 million) of pre-aligned nucleotide sequences. It performs the clustering of sequences using the Hierarchical Clustering Algorithm (HCA). There are currently three different cluster metrics implemented: single-linkage, complete-linkage, and average-linkage. In addition, there are currently four sequence distance functions implemented, these are: identity (gap-gap counting as match), nogap (gap-gap being ignored), nogap-single (like nogap, but consecutive gap-nogap''s count as a single mismatch), tamura (distance is calculated with the knowledge that transitions are more likely than transversions). One advantage that HCA has over other algorithms is that instead of producing only the clustering at a given threshold, it produces the set of merges occuring at each threshold. With this approach, the clusters can afterwards very quickly be reported for every arbitrary threshold with little extra computation. This approach also allows the plotting of the variation of number of clusters with clustering threshold without requiring the clustering to be run for each threshold independently. Another feature of the way HPC-CLUST is implemented is that the single-, complete-, and average-linkage clusterings can be computed in a single run with little overhead. | c++, mpi |
is listed by: OMICtools has parent organization: University of Zurich; Zurich; Switzerland |
PMID:24215029 | OMICS_01446 | SCR_005052 | 2026-02-14 02:00:48 | 5 | ||||||||
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M-pick Resource Report Resource Website |
M-pick (RRID:SCR_004995) | M-pick | software resource | A modularity-based clustering software for Operational Taxonomic Unit (OTU) picking of 16S rRNA sequences. The algorithm does not require a predetermined cut-off level, and our simulation studies suggest that it is superior to existing methods that require specified distance or variance levels to define OTUs. | 16s rrna sequence, 16s rrna, rrna, sequence, binning |
is listed by: OMICtools has parent organization: University of Florida; Florida; USA |
OMICS_01447 | SCR_004995 | M-pick: a modularity-based clustering method for OTU picking | 2026-02-14 02:01:01 | 0 | ||||||||
|
University of Manchester; Manchester; United Kingdom Resource Report Resource Website 1+ mentions |
University of Manchester; Manchester; United Kingdom (RRID:SCR_004996) | university | Public research university in Manchester, England, formed in 2004 by merger of University of Manchester Institute of Science and Technology and Victoria University of Manchester. Second largest university in United Kingdom by enrollment. |
is affiliated with: OpenMinTeD is related to: NEWMEDS is related to: ORBITO is related to: Open PHACTS is related to: EMIF is parent organization of: Smart Dictionary Lookup is parent organization of: mlgt is parent organization of: Utopia Docs is parent organization of: Kidney and Urinary Pathway Knowledge Base is parent organization of: PUMA is parent organization of: DOSY Toolbox is parent organization of: RightField is parent organization of: SEEK is parent organization of: miRBase is parent organization of: PRINTS is parent organization of: CHEM21 is parent organization of: Taverna is parent organization of: SysMO-DB is parent organization of: MethodBox is parent organization of: OWL API is parent organization of: X:MAP is parent organization of: Mimas is parent organization of: National Centre for Text Mining is parent organization of: Chemistry Using Text Annotations is parent organization of: TerMine is parent organization of: Acromine Disambiguator is parent organization of: Census Dissemination Unit is parent organization of: Open Regulatory Annotation Database is parent organization of: ADAPT: A Database of Affymetrix Probesets and Transcripts is parent organization of: brat rapid annotation tool is parent organization of: UK DNA Banking Network is parent organization of: AcroMine is parent organization of: BioIE: Extracting Informative Sentences From the Biomedical Literature is parent organization of: Biocatalogue - The Life Science Web Services Registry is parent organization of: myExperiment is parent organization of: Software Ontology is parent organization of: bioNerDS is parent organization of: MorphoJ is parent organization of: University of Manchester Bioinformatics Core Facility is parent organization of: miRBase is parent organization of: Simple Assignment of Spots to Surfaces is parent organization of: AMBER parameter database is parent organization of: University of Manchester Electron Microscopy Core Facility is parent organization of: University of Manchester Mass Spectrometry and Separations Core Facility is parent organization of: University of Manchester Advanced Manufacturing Platform Core Facility is parent organization of: University of Manchester Surface Characterisation Core Facility is parent organization of: University of Manchester Biochemical and Biophysical Sciences Technology Platform Core Facility is parent organization of: University of Manchester Corrosion and Materials for Demanding Environments Core Facility is parent organization of: University of Manchester Magnetic Resonance and Related Technology Platform Core Facility is parent organization of: University of Manchester X-ray Diffraction Platform Core Facility is parent organization of: University of Manchester Services and Equipment Core Facility is parent organization of: University of Manchester Design, Fabrication and Testing Core Facility is parent organization of: University of Manchester National X-ray Computed Tomography Core Facility is parent organization of: University of Manchester Advanced Metal Development Core Facility |
nlx_74265, Wikidata:Q230899, grid.5379.8, ISNI:121662407, Crossref funder ID:501100000770 | https://ror.org/027m9bs27 | SCR_004996 | University of Manchester | 2026-02-14 02:00:49 | 7 | |||||||||
|
Bio X Cell Resource Report Resource Website 1000+ mentions |
Bio X Cell (RRID:SCR_004997) | commercial organization | Commercial supplier and developer of in vivo antibodies. Provides antibodies and antibody production services. | commercial, antibody, reagent, biomedical, research, new hampshire, | SCR_019248, nlx_152318 | SCR_004997 | 2026-02-14 02:01:03 | 4386 | |||||||||||
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ESPRIT-Tree Resource Report Resource Website 1+ mentions |
ESPRIT-Tree (RRID:SCR_005045) | ESPRIT-Tree | software resource | Software for hierarchical Clustering Analysis of Millions of 16S rRNA Pyrosequences in Quasi-linear Time. | clustering, 16s rrna, pyrosequence |
is listed by: OMICtools has parent organization: University of Florida; Florida; USA |
PMID:21596775 | OMICS_01445 | SCR_005045 | ESPRIT-Tree: Hierarchical Clustering Analysis of Millions of 16S rRNA Pyrosequences in Quasi-linear Time | 2026-02-14 02:01:03 | 9 | |||||||
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Huazhong University of Science and Technology; Wuhan; China Resource Report Resource Website |
Huazhong University of Science and Technology; Wuhan; China (RRID:SCR_005047) | HUST | university | Public research university located in Guanshan Subdistrict, Hongshan District, Wuhan, Hubei province, China. |
is parent organization of: AnimalTFDB is parent organization of: Midbody, Centrosome and Kinetochore is parent organization of: EPSD Eukaryotic Phosphorylation Site Database |
ISNI:0000 0004 0368 7223, grid.33199.31, Wikidata:Q1711196, nlx_144495, Crossref funder ID:501100003397 | https://ror.org/00p991c53 | SCR_005047 | Huazhong University of Science and Technology, Huazhong University of Science & Technology, Huazhong University of Science & Technology; Hubei; China | 2026-02-14 02:00:48 | 0 | ||||||||
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Charles University; Prague; Czech Republic Resource Report Resource Website 1+ mentions |
Charles University; Prague; Czech Republic (RRID:SCR_002931) | CU | university | Research university located in Prague, Czech Republic. | university, research university, degree |
is parent organization of: IRESite is parent organization of: Database of Germline p53 Mutations is parent organization of: Culture Collection of Fungi is parent organization of: IRESite is parent organization of: Charles University Vinicna Microscopy Core Facility |
nlx_87455, ISNI 0000 0004 1937 116X, Crossref Funder ID 100007397, Wikidata Q31519, GRID grid.4491.8 | https://ror.org/024d6js02 | SCR_002931 | Charles University, Charles University in Prague, Univerzita Karlova | 2026-02-14 02:00:28 | 7 | |||||||
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Genox Corpooration Resource Report Resource Website |
Genox Corpooration (RRID:SCR_002930) | commercial organization | Biotechnological company that produces and supplies materials to oxidative stress and aging researchers. | oxidative stress, biomarker, antibody | nlx_152373 | SCR_002930 | 2026-02-14 02:00:35 | 0 | |||||||||||
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Time-series RNA-seq Analysis Package Resource Report Resource Website 1+ mentions |
Time-series RNA-seq Analysis Package (RRID:SCR_002935) | TRAP | software resource | A comprehensive software package integrating all necessary tasks such as mapping short reads, measuring gene expression levels, finding differentially expressed genes (DEGs), clustering and pathway analysis for time-series data in a single environment. | time-series, rna-seq, analysis |
is listed by: OMICtools has parent organization: Seoul National University; Seoul; South Korea |
PMID:24518221 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02590 | SCR_002935 | 2026-02-14 02:00:35 | 3 | |||||||
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GenScript Resource Report Resource Website 5000+ mentions |
GenScript (RRID:SCR_002891) | commercial organization | Commercial organization which provides life science services and products to researchers. They specialize in gene synthesis, peptide, protein, antibody and preclinical drug development service. | gene synthesis service, drug development, reagent provider | nlx_152374 | http://www.dddmag.com/company-profiles/genscript-usa-inc | SCR_002891 | GenScript USA, GenScript USA Inc | 2026-02-14 02:00:20 | 7067 | |||||||||
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pBuild Resource Report Resource Website 1+ mentions |
pBuild (RRID:SCR_002929) | software resource | A software tool that can compare several search engines' results and combine them together. | mass spectrometry, proteomics |
is listed by: OMICtools has parent organization: Chinese Academy of Sciences; Beijing; China |
OMICS_02468 | SCR_002929 | 2026-02-14 02:00:20 | 8 | ||||||||||
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National Postdoctoral Association Resource Report Resource Website 1+ mentions |
National Postdoctoral Association (RRID:SCR_002928) | NPA | institution | Representative organization for postdoctoral scholars in the United States. It is member-driven and non-profit. | representation, post doc, postdoctoral scholar | Restricted | nif-0000-00476, grid.436397.c | https://ror.org/01gsm0s82 | SCR_002928 | National Postdoctoral Association | 2026-02-14 02:00:35 | 7 | |||||||
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aCGH.Spline Resource Report Resource Website |
aCGH.Spline (RRID:SCR_002927) | software resource | An R package for array comparative genomic hybridization (aCGH) dye bias normalization. | standalone software, mac os x, unix/linux, windows, r |
is listed by: OMICtools has parent organization: CRAN |
PMID:21357574 | Free, Available for download, Freely available | OMICS_02607 | http://cran.r-project.org/web/packages/aCGH.Spline/ | SCR_002927 | 2026-02-14 02:00:28 | 0 | |||||||
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StreamingTrim Resource Report Resource Website 1+ mentions |
StreamingTrim (RRID:SCR_002922) | software resource | A DNA reads trimming software, written in Java, with which researchers are able to analyse the quality of DNA sequences in fastq files and to search for low-quality zones in a very conservative way. | standalone software, java, 16s rrna, sequence | is listed by: OMICtools | PMID:24128146 | Free, Available for download, Freely available | OMICS_05196 | SCR_002922 | 2026-02-14 02:00:35 | 8 |
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