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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
vipR Resource Report Resource Website 50+ mentions |
vipR (RRID:SCR_010685) | vipR | software resource | A software program to screen for sequence variants (SNPs, deletions) in sequence data generated by high-throughput-sequencing platforms. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00081 | SCR_010685 | 2026-08-29 11:23:50 | 60 | ||||||||||
|
MaSuRCA Resource Report Resource Website 100+ mentions |
MaSuRCA (RRID:SCR_010691) | MaSuRCA | software resource | A whole genome assembly software that combines the efficiency of the de Bruijn graph and Overlap-Layout-Consensus (OLC) approaches., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Maryland; Maryland; USA |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00020, biotools:masurca | https://bio.tools/masurca | SCR_010691 | 2026-08-29 11:23:45 | 468 | |||||||
|
Gossamer Resource Report Resource Website 1+ mentions |
Gossamer (RRID:SCR_010612) | Gossamer | software resource | A software application for the de novo assembly of genomes from fragments of DNA that specifically attacks the question of scalability. | is listed by: OMICtools | OMICS_00017 | SCR_010612 | Gossamer: A Space-Efficient Genome Assembler | 2026-08-29 11:23:49 | 1 | |||||||||
|
ABySS Resource Report Resource Website 500+ mentions |
ABySS (RRID:SCR_010709) | ABySS | data analysis software, data processing software, sequence analysis software, software application, software resource | Software providing de novo, parallel, paired-end sequence assembler that is designed for short reads. ABySS 1.0 originally showed that assembling human genome using short 50 bp sequencing reads was possible by aggregating half terabyte of compute memory needed over several computers using standardized message passing system. ABySS 2.0 is Resource Efficient Assembly of Large Genomes using Bloom Filter. ABySS 2.0 departs from MPI and instead implements algorithms that employ Bloom filter, probabilistic data structure, to represent de Bruijn graph and reduce memory requirements. | paired-end sequence assembler, short reads, assembling human genome, large genomes, bloom filter, |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite |
British Columbia Cancer Foundation ; Genome British Columbia ; Genome Canada ; NHGRI R01HG007182 |
PMID:19251739 DOI:10.1101/068338 DOI:10.1101/gr.214346.116 |
Free, Available for download, Freely available | OMICS_00006, biotools:abyss | https://github.com/bcgsc/abyss, https://sources.debian.org/src/abyss/, https://bio.tools/abyss, | SCR_010709 | ABySS 1.0, ABySS 2.0 | 2026-08-29 11:23:35 | 808 | ||||
|
Meraculous Resource Report Resource Website 10+ mentions |
Meraculous (RRID:SCR_010700) | Meraculous | software resource | An algorithm for de novo genome assembly with short paired-end reads. | is listed by: OMICtools | OMICS_00021 | SCR_010700 | Meraculous: De Novo Genome Assembly with Short Paired-End Reads | 2026-08-29 11:23:45 | 39 | |||||||||
|
ContextMap Resource Report Resource Website 10+ mentions |
ContextMap (RRID:SCR_010496) | ContextMap | software resource | A context-based approach to identify the most likely mapping for RNA-seq experiments. | is listed by: OMICtools | OMICS_01239 | SCR_010496 | 2026-08-29 11:23:32 | 28 | ||||||||||
|
CRAC Resource Report Resource Website 10+ mentions |
CRAC (RRID:SCR_010652) | CRAC | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Integrated RNA-Seq read analysis., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. |
is listed by: OMICtools is listed by: Debian |
DOI:10.1186/s12920-016-0178-5 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01240 | https://sources.debian.org/src/crac/ | SCR_010652 | 2026-08-29 11:23:44 | 16 | |||||||
|
Geneious Resource Report Resource Website 10000+ mentions |
Geneious (RRID:SCR_010519) | data analysis software, data management software, data processing software, sequence analysis software, software application, software resource, software toolkit | Software package for sequence alignment, assembly and analysis. Integrated and extendable desktop software platform for organization and analysis of sequence data. Bioinformatics software platform packed with molecular biology and sequence analysis tools. | Sequence alignment software, data management software, analysis software, Geneious Biologics, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite is parent organization of: Geneious Microsatellite Plugin |
PMID:22543367 | Restricted | OMICS_00016, biotools:geneious | http://nebc.nerc.ac.uk/news/geneiousonbl, https://bio.tools/geneious | SCR_010519 | Geneious Prime, Geneious 11.0, Geneious 11.1.2, Geneious 8.1, Geneious Basic | 2026-08-29 11:23:43 | 13589 | ||||||
|
miRTar Resource Report Resource Website 50+ mentions |
miRTar (RRID:SCR_010851) | miRTar | analysis service resource, data analysis service, data or information resource, data set, production service resource, service resource | An integrated web server for identifying miRNA-target interactions in human. The tool enables biologists easily to identify the biological functions and regulatory relationships between a group of known/putative miRNAs and protein coding genes. It also provides perspective of information on the miRNA targets on alternatively spliced transcripts. |
is listed by: OMICtools has parent organization: National Chiao Tung University; Hsinchu; Taiwan |
OMICS_00410 | SCR_010851 | MicroRNA Target prediction | 2026-08-29 11:23:56 | 55 | |||||||||
|
CoRAL - Classification of RNAs by Analysis of Length Resource Report Resource Website 10+ mentions |
CoRAL - Classification of RNAs by Analysis of Length (RRID:SCR_010828) | CoRAL | software resource | A machine learning software package that can predict the precursor class of small RNAs present in a high-throughput RNA-sequencing dataset. In addition to classification, it also produces information about the features that are most important for discriminating different populations of small non-coding RNAs. |
is listed by: OMICtools has parent organization: University of Pennsylvania; Philadelphia; USA |
PMID:23700308 | Acknowledgement requested | OMICS_00372 | SCR_010828 | Classification of RNAs by Analysis of Length | 2026-08-29 11:23:38 | 11 | |||||||
|
PriVar Resource Report Resource Website 1+ mentions |
PriVar (RRID:SCR_010784) | PriVar | software resource | A toolkit for prioritizing SNVs and indels from next-generation sequencing data. | is listed by: OMICtools | OMICS_00160 | SCR_010784 | 2026-08-29 11:23:37 | 2 | ||||||||||
|
CNVer Resource Report Resource Website 1+ mentions |
CNVer (RRID:SCR_010820) | CNVer | software resource | A method for CNV detection that supplements the depth-of-coverage with paired-end mapping information, where matepairs mapping discordantly to the reference serve to indicate the presence of variation. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
biotools:cnver, OMICS_00341 | https://bio.tools/cnver | SCR_010820 | 2026-08-29 11:23:55 | 8 | ||||||||
|
CNVnator Resource Report Resource Website 500+ mentions |
CNVnator (RRID:SCR_010821) | CNVnator | software resource | An approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing. | is listed by: OMICtools | OMICS_00343 | SCR_010821 | 2026-08-29 11:23:47 | 547 | ||||||||||
|
Diplotyper Resource Report Resource Website |
Diplotyper (RRID:SCR_010789) | Diplotyper | software resource | A fully automated software tool which is available for Linux to investigate associations between a diplotype group and a phenotype in linear or logistic regression. |
is listed by: OMICtools has parent organization: Google Code |
OMICS_00195 | SCR_010789 | 2026-08-29 11:23:54 | 0 | ||||||||||
|
Control-FREEC Resource Report Resource Website 100+ mentions |
Control-FREEC (RRID:SCR_010822) | Control-FREEC | software resource | Prediction of copy number alterations and loss of heterozygosity using deep-sequencing data. | is listed by: OMICtools | OMICS_00344 | SCR_010822 | 2026-08-29 11:23:38 | 346 | ||||||||||
|
readDepth Resource Report Resource Website 10+ mentions |
readDepth (RRID:SCR_010824) | readDepth | software resource | This package for R can detect copy number aberrations by measuring the depth of coverage obtained by massively parallel sequencing of the genome. | is listed by: OMICtools | OMICS_00350 | SCR_010824 | 2026-08-29 11:23:47 | 23 | ||||||||||
|
HapCUT Resource Report Resource Website 10+ mentions |
HapCUT (RRID:SCR_010791) | HapCUT | software resource | A max-cut based algorithm for haplotype assembly using sequence reads from the two chromosomes of an individual. | is listed by: OMICtools | OMICS_00198 | SCR_010791 | 2026-08-29 11:23:37 | 17 | ||||||||||
|
Relate Resource Report Resource Website 10+ mentions |
Relate (RRID:SCR_010794) | Relate | software resource | Software providing a method that estimates the probability of sharing alleles identity by descent (IBD) across the genome and can also be used for mapping disease loci using distantly related individuals. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:19025785 | biotools:relateadmix, OMICS_00207 | https://bio.tools/relateadmix | SCR_010794 | 2026-08-29 11:23:37 | 47 | |||||||
|
RNAsnp Resource Report Resource Website 10+ mentions |
RNAsnp (RRID:SCR_010837) | RNAsnp | analysis service resource, data analysis service, production service resource, service resource, software resource | Software / Web Server to predict the effect of SNPs on local RNA secondary structure based on the RNA folding algorithms implemented in the Vienna RNA package. |
is listed by: OMICtools has parent organization: University of Copenhagen; Copenhagen; Denmark |
PMID:23630321 | OMICS_00392 | SCR_010837 | RNAsnp Web Server, RNAsnp Web Server: Predicting SNP effects on local RNA secondary structure | 2026-08-29 11:23:56 | 34 | ||||||||
|
BCmicrO Resource Report Resource Website 1+ mentions |
BCmicrO (RRID:SCR_010838) | BCmicrO | software resource, web application | A Bayesian decision fusion algorithm for microRNA target prediction that combines the prediction of TargetScan, miRanda, PicTar, mirTarget, PITA, and DianamicroT. Users enter a Ref_seq ID for a query target gene and select a miRNA, which BCmicrO will use in its predictive algorithm. The prediction results can then be downloaded. | mirna, microrna, bayesian, decision fusion algorithm, computational target prediction algorithm, web application, |
is listed by: OMICtools has parent organization: University of Texas at San Antonio; Texas; USA |
Public | OMICS_00393 | SCR_010838 | 2026-08-29 11:23:47 | 8 |
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