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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
T-REKS Resource Report Resource Website 10+ mentions |
T-REKS (RRID:SCR_010768) | T-REKS | software resource | An algorithm for de novo detection and alignment of repeats in sequences based on K-means algorithm. | matlab | is listed by: OMICtools | PMID:19671691 | OMICS_00116 | SCR_010768 | 2026-08-29 11:23:53 | 18 | ||||||||
|
GensearchNGS Resource Report Resource Website 10+ mentions |
GensearchNGS (RRID:SCR_010802) | GensearchNGS | software resource | An integrated software solution for the analysis of DNA-Seq data from commonly used NGS equipments such as Roche/454, Illumina and Ion Torrent. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
Commercial license | OMICS_00287, biotools:gensearchngs | https://bio.tools/gensearchngs | SCR_010802 | 2026-08-29 11:23:46 | 23 | |||||||
|
AgileVariantMapper Resource Report Resource Website 1+ mentions |
AgileVariantMapper (RRID:SCR_010770) | AgileVariantMapper | software resource | Software that visualises sequence variant data from whole exome data, so that it is possible to identify autozygous regions in consanguineous individuals. | is listed by: OMICtools | PMID:23090942 | OMICS_00122 | SCR_010770 | AgileVariantMapper - Autozygosity mapping using Next generation sequence data | 2026-08-29 11:23:36 | 1 | ||||||||
|
HomSI Resource Report Resource Website 1+ mentions |
HomSI (RRID:SCR_010771) | HomSI | software resource | A software tool that identifies homozygous regions using deep sequence data. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:24307702 | Free | OMICS_00124, biotools:homsi | https://bio.tools/homsi | SCR_010771 | Homozygous Stretch Identifier from next-generation sequencing data, HomSI - Homozygous Stretch Identifier from next-generation sequencing data | 2026-08-29 11:23:53 | 4 | |||||
|
CONTRA Resource Report Resource Website 100+ mentions |
CONTRA (RRID:SCR_010814) | CONTRA | software resource | A tool for copy number variation (CNV) detection for targeted resequencing data such as those from whole-exome capture data. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
OMICS_00331, biotools:contra | https://bio.tools/contra | SCR_010814 | 2026-08-29 11:23:55 | 291 | ||||||||
|
ExomeCNV Resource Report Resource Website 50+ mentions |
ExomeCNV (RRID:SCR_010815) | ExomeCNV | software resource | A statistical method to detect CNV and LOH using depth-of-coverage and B-allele frequencies from mapped short sequence reads in exome sequencing data. | is listed by: OMICtools | OMICS_00333 | SCR_010815 | 2026-08-29 11:23:46 | 62 | ||||||||||
|
CNAnorm Resource Report Resource Website 10+ mentions |
CNAnorm (RRID:SCR_010816) | CNAnorm | software resource | A Bioconductor package to estimate Copy Number Aberrations (CNA) in cancer samples. | is listed by: OMICtools | OMICS_00336 | SCR_010816 | 2026-08-29 11:23:38 | 16 | ||||||||||
|
CNValidator Resource Report Resource Website |
CNValidator (RRID:SCR_010819) | CNValidator | software resource | Identifies high quality CNVs based on the density of homozygous SNPs and the ratio of heterozygous SNP reads. |
is listed by: OMICtools has parent organization: Google Code |
OMICS_00340 | SCR_010819 | cnvalidator - a package for identification of high quality copy-number variations | 2026-08-29 11:23:38 | 0 | |||||||||
|
breseq Resource Report Resource Website 100+ mentions |
breseq (RRID:SCR_010810) | breseq | software resource | A computational pipeline for finding mutations relative to a reference sequence in short-read DNA re-sequencing data intended for haploid microbial genomes. | windows, genomics, sequencing, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Google Code |
OMICS_00298, biotools:breseq | https://barricklab.org/twiki/bin/view/Lab/ToolsBacterialGenomeResequencing, https://bio.tools/breseq | SCR_010810 | breseq - Determine mutations in evolved microbes from next-generation sequencing data | 2026-08-29 11:23:38 | 474 | |||||||
|
MutPred Resource Report Resource Website 100+ mentions |
MutPred (RRID:SCR_010778) | MutPred | software resource, web application | Web application tool developed to classify an amino acid substitution as disease-associated or neutral in human. | bio.tools |
is used by: HmtVar is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Indiana University; Indiana; USA |
biotools:mutpred, OMICS_00154 | https://bio.tools/mutpred | SCR_010778 | 2026-08-29 11:23:37 | 470 | ||||||||
|
MutSig Resource Report Resource Website 100+ mentions |
MutSig (RRID:SCR_010779) | MutSig | software resource | Software that analyzes lists of mutations discovered in DNA sequencing, to identify genes that were mutated more often than expected by chance given background mutation processes. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Broad Institute |
PMID:23770567 | OMICS_00155, biotools:MutSig2CV | https://bio.tools/MutSig2CV | SCR_010779 | Mutation Significance | 2026-08-29 11:23:53 | 129 | ||||||
|
SVDetect Resource Report Resource Website 10+ mentions |
SVDetect (RRID:SCR_010812) | SVDetect | software resource | Software application for the isolation and the type prediction of intra- and inter-chromosomal rearrangements from paired-end/mate-pair sequencing data provided by the high-throughput sequencing technologies. This tool aims to identify structural variations with both clustering and sliding-window strategies, and helping in their visualization at the genome scale. It is compatible with SOLiD and Illumina (>=1.3) reads. | structural variation, sequencing, chromosomal rearrangement, high-throughput sequencing, solid, illumina, genome, insertion, deletion, inversion, duplication, translocation, command-line, perl, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge has parent organization: Curie Institute; Paris; France |
PMID:20639544 | GNU General Public License, v3 | OMICS_00324, biotools:svdetect | https://bio.tools/svdetect | SCR_010812 | SVDetect: a tool to detect genomic structural variations from paired-end and mate-pair sequencing data | 2026-08-29 11:23:46 | 24 | |||||
|
nsSNPAnalyzer Resource Report Resource Website 50+ mentions |
nsSNPAnalyzer (RRID:SCR_010780) | nsSNPAnalyzer | analysis service resource, data analysis service, data analysis software, data processing software, production service resource, service resource, software application, software resource | A tool to predict whether a nonsynonymous single nucleotide polymorphism (nsSNP) has a phenotypic effect. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Tennessee Health Science Center; Tennessee; USA |
OMICS_00156, biotools:nssnpanalyzer | https://bio.tools/nssnpanalyzer | SCR_010780 | nsSNPAnalyzer: predicting disease-associated nonsynonymous single nucleotide polymorphisms | 2026-08-29 11:23:46 | 50 | |||||||
|
PhD-SNP Resource Report Resource Website 100+ mentions |
PhD-SNP (RRID:SCR_010782) | PhD-SNP | software resource | It is based a SVM-based classifier. | is listed by: OMICtools | PMID:16895930 | OMICS_00158 | SCR_010782 | Predictor of human Deleterious Single Nucleotide Polymorphisms | 2026-08-29 11:23:53 | 335 | ||||||||
|
PMut Resource Report Resource Website 50+ mentions |
PMut (RRID:SCR_010783) | PMut | software resource | A software aimed at the annotation and prediction of pathological mutations. | is listed by: OMICtools | PMID:15390262 | OMICS_00159 | SCR_010783 | 2026-08-29 11:23:46 | 80 | |||||||||
|
Medical Biobank Resource Report Resource Website |
Medical Biobank (RRID:SCR_010748) | Medical Biobank | biospecimen repository, material storage repository, service resource, storage service resource | A biobank created from a cross-sectional population of a town in Sweden. The Medical Biobank is mainly based on three cohorts: The V��sterbotten intervention cohort, the MONICA-cohort, and the Mammary screening cohort. These sub-cohorts together are named Northern Sweden Health and Disease Study Cohort (North Health). These sub-cohorts together is named Northern Sweden Health and Disease Study Cohort (North Health). Originally, the V��sterbotten Intervention program (VIP) is a long-term project intended for health promotion of the population of V��sterbotten. All individuals 40, 50 and 60 years of age in the population of the county are invited for screening (approx. 254.000 inhabitants). They are asked to complete a questionnaire concerning various lifestyle factors including diet. They are also asked to donate a separate blood sample to the Medical Biobank for freeze storage for later research purposes. The project started in 1985 and the cohort covered in December 2002, 74,000 individuals, of whom 67,000 had donated blood samples. The material is supplemented with population based samples from a local mammary screening (44,000 sampling occasions, 25,700 unique individuals) and from the Northern Sweden MONICA Project (11,500 sampling occasions, 7,500 unique individuals). The total cohort contains at the moment 85.000 unique individuals with 130.000 sampling occasions. The VIP and MONICA cohorts are population based and the mammary screening cohort are nearly population based. Follow-up: * For the VIP-cohort a second sample (and questionnaire) is collected with a 10-year interval of the individuals within the cohort. * Repeated sampling was performed in the MONICA project in 1999 on individuals participating in 1986, 1990, and 1994. * From 1997 repeated screening has started within the mammary screening program with sampling every second year, in the age group 50-69 years within the county. Biobank content: * Life-Style Questionnaire: Every attending subject is asked to answer a questionnaire, which in the VIP and MONICA-projects includes questions about education, occupation/working conditions, daily habits including smoking, diet, etc and in the mammary screening cohort on reproductive conditions. The dietary questionnaire has been validated twice. The data from the questionnaires, as well as from results from the biobank, are kept in a database for future research purposes. The questionnaires in the VIP and the MONICA project are optically read. * Measurements: Blood Pressure, Anthropometry, Glucose Tolerance Test, Blood Lipids * Blood Samples: The attendants are asked for their willingness to donate a sample of 20-ml whole blood for future analyses. The sample is taken after 4 hours of fasting or in the morning after an over night fasting (most samples) in the VIP and MONICA cohorts. The 20-ml sample is divided into 10 subsamples consisting of 6 plasma, 2 leukocyte (buffy coat) and 2 erythrocyte samples. All material is frozen at -80 degrees C. The organization of the bank is elaborated with specially trained staff and an organization of transport-, storage- and security facilities. For DNA handling a specialized laboratory has been built up. * End-points: Mortality, Cancer events, Cardiovascular events, Other morbidity, Other registry-based follow-up * Registries: At regular intervals the cohort is scanned for incident myocardial infarctions (MI) and stroke utilizing the Northern Sweden MONICA registry and for cancer using the regional cancer registry. In the future the same procedure will be applied also on other registries e.g. diabetes, osteoporosis, dementia. | lifestyle, diet, adult, questionnaire |
is listed by: One Mind Biospecimen Bank Listing is related to: Swedish National Biobank Program has parent organization: Umea University; Umea; Sweden |
General adult population, (40 50 and 60 years of age), Adult, Middle adult human, Aging | Public: The Medical Biobank has been positioned as a national and international resource for scientific research. All applications must be: Approved by the Board of Experts, Research Ethics Committee and Medical Biobank. | nlx_99793 | SCR_010748 | Biobank of Northern Sweden | 2026-08-29 11:23:36 | 0 | ||||||
|
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 | 2026-08-29 11:23:35 | 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 | 2026-08-29 11:23:52 | 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 | 2026-08-29 11:23:52 | 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 | 2026-08-29 11:23:36 | 1342 |
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