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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Eagle Resource Report Resource Website 50+ mentions |
Eagle (RRID:SCR_015991) | software resource, software toolkit | Software package for statistical estimation of haplotype phase either within a genotyped cohort or using a phased reference panel in large scale sequencing. The package includes Eagle1 (to harness identity-by-descent among distant relatives to rapidly call phase using a fast scoring approach) and Eagle2 (to analyze a full probabilistic model similar to the diploid Li-Stephens model used by previous HMM-based methods. | hmm, hidden markov model, statistic, estimation, haplotype, phase, reference, panel, sequencing, algorithm, analysis, probability |
is listed by: Debian is listed by: OMICtools has parent organization: Broad Institute |
NHGRI R01 HG006399; NIMH R01 MH101244; NHGRI F32HG007805; Wellcome Trust WT098051; Austrian Science Fund J-3401; NHGRI HG007022; NHLBI HL117626; Fannie and John Hertz Foundation ; NCRR S10 RR028832; NWO 480-05-003; Dutch Brain Foundation |
PMID:27694958 PMID:27270109 |
Free, Available for download, Freely available | OMICS_14099, SCR_017262 | https://sources.debian.org/src/bio-eagle/, https://github.com/poruloh/Eagle, https://data.broadinstitute.org/alkesgroup/Eagle/downloads/ | SCR_015991 | Bio-eagle, Eagle1, Eagle2 | 2026-08-08 12:05:15 | 57 | |||||
|
ABACAS Resource Report Resource Website 100+ mentions |
ABACAS (RRID:SCR_015852) | ABACAS | software resource, software application | Software that contiguates (align, order, orientate), visualizes and designs primers to close gaps on shotgun assembled contigs based on a reference sequence. ABACAS finds alignment positions and identifies syntenies of assembled contigs against the reference, then generates a pseudomolecule taking overlapping contigs and gaps into account. | contiguation, primer, shotgun assembled contig, reference sequence, assembled sequence |
is listed by: Debian is listed by: OMICtools |
European Union LSHP-LT-2004-503578; Wellcome Trust Sanger Institute |
Free, Available for download | OMICS_06933 | https://sourceforge.net/projects/abacas/files/, https://sources.debian.org/src/abacas/ | SCR_015852 | ABACAS: Algorithm Based Automatic Contiguation of Assembled Sequences, Algorithm Based Automatic Contiguation of Assembled Sequences (ABACAS), Algorithm Based Automatic Contiguation of Assembled Sequences | 2026-08-08 12:05:15 | 178 | |||||
|
Ecopcr Resource Report Resource Website 10+ mentions |
Ecopcr (RRID:SCR_016082) | Ecopcr | software resource, software application | Software for Electronic PCR that estimates PCR barcode primers quality and develops new barcode primers. In conjunction with OBITools, users can postprocess ecoPCR output to compute barcode coverage and barcode specificity., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | electronic, PCR, estimate, primers, quality, barcode |
is listed by: Debian is listed by: OMICtools |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_19861 | https://sources.debian.org/src/ecopcr/ | http://www.grenoble.prabi.fr/trac/ecoPCR/ | SCR_016082 | Ecopcr: Electronic polymerase chain reaction | 2026-08-08 12:05:20 | 27 | |||||
|
Concavity Resource Report Resource Website 50+ mentions |
Concavity (RRID:SCR_016063) | software toolkit, software resource, software application | Software for predicting protein ligand binding sites that integrate evolutionary sequence conservation estimates with structure-based methods for identifying protein surface cavities. Used in predicting catalytic sites and drug binding pockets. | predict, protein, ligand, binding, site, catalytic, drug, algorithm |
is listed by: Debian is listed by: OMICtools is related to: Princeton University; New Jersey; USA |
PMID:19997483 DOI:10.1371/journal.pcbi.1000585 |
Free, Available for download | OMICS_04161 | http://manpages.ubuntu.com/manpages/bionic/man1/concavity.1.html, https://sources.debian.org/src/concavity/ | SCR_016063 | 2026-08-08 12:05:24 | 94 | |||||||
|
DNAPlotter Resource Report Resource Website 100+ mentions |
DNAPlotter (RRID:SCR_005006) | DNAPlotter | software resource, software application | Software application used to generate images of circular and linear DNA maps to display regions and features of interest. The images can be inserted into a document or printed out directly. As this uses Artemis it can read in the common file formats EMBL, GenBank and GFF3. | java, circular, linear, plot, genome, macosx, unix, windows |
is listed by: OMICtools is related to: Artemis: Genome Browser and Annotation Tool has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
PMID:18990721 | GNU General Public License | OMICS_00906, nlx_96278 | SCR_005006 | DNAPlotter: circular and linear interactive genome visualization | 2026-08-08 12:04:57 | 110 | ||||||
|
CloVR Resource Report Resource Website 10+ mentions |
CloVR (RRID:SCR_005290) | CloVR | software resource, service resource | A desktop application for push-button automated sequence analysis that can utilize cloud computing resources. CloVR is implemented as a single portable virtual machine (VM) that provides several automated analysis pipelines for microbial genomics, including 16S, whole genome and metagenome sequence analysis. The CloVR VM runs on a personal computer, utilizes local computer resources and requires minimal installation, addressing key challenges in deploying bioinformatics workflows. In addition CloVR supports use of remote cloud computing resources to improve performance for large-scale sequence processing. | cloud computing, next-generation sequencing |
is listed by: OMICtools has parent organization: University of Maryland; Maryland; USA |
Amazon Web Services in Education Research Grants program ; National Human Genome Research Institute ; NHGRI RC2 HG005597-01; NSF 0949201 |
PMID:21878105 | OMICS_01216 | SCR_005290 | CloVR - Automated Sequence Analysis from Your Desktop, Cloud Virtual Resource | 2026-08-08 12:04:47 | 26 | ||||||
|
VAGrENT Resource Report Resource Website 10+ mentions |
VAGrENT (RRID:SCR_005180) | VAGrENT | software resource, software toolkit | Software tool set for calculating the biological consequences of genomic variations. The suite of perl modules compares genomic variations with reference genome annotations and generates the possible effects each variant may have on the transcripts it overlaps. It evaluates each variation/transcript combination and describes the effects in the mRNA, CDS and protein sequence contexts. It provides details of the sequence and position of the change within the transcript / protein as well as Sequence Ontology terms to classify its consequences. | perl, genomic variation, transcript, mrna, cds, protein sequence, protein, sequence |
is listed by: OMICtools is related to: SO has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
OMICS_00192 | SCR_005180 | VAGrENT: Variation Annotation Generator, Variation Annotation Generator | 2026-08-08 12:04:56 | 17 | ||||||||
|
GeneNetworkBuilder Resource Report Resource Website 1+ mentions |
GeneNetworkBuilder (RRID:SCR_006455) | GeneNetworkBuilder | software resource, software application | Software application for discovering direct or indirect targets of transcription factors (TFs) using ChIP-chip or ChIP-seq, and microarray or RNA-seq gene expression data. Inputting a list of genes of potential targets of one TF from ChIP-chip or ChIP-seq, and the gene expression results, it generates a regulatory network of the TF. | transcription factor, graph, network, microarray, sequencing, chip-chip, chip-seq, gene expression, regulatory network, target |
is listed by: OMICtools has parent organization: Bioconductor |
GNU General Public License, v2 or greater | OMICS_00806, OMICS_01971 | http://www.bioconductor.org/packages/release/bioc/html/GeneNetworkBuilder.html | SCR_006455 | GeneNetworkBuilder - Build Regulatory Network from ChIP-chip/ChIP-seq and Expression Data | 2026-08-08 12:04:50 | 2 | ||||||
|
Google App Engine Resource Report Resource Website 1+ mentions |
Google App Engine (RRID:SCR_006496) | Google App Engine | service resource, software resource, software application, software development tool | Platform as a service that provides a fully-integrated application environment that permits web applications to run on Google''s infrastructure. The environment includes: dynamic web serving, with full support for common web technologies, persistent storage with queries, sorting and transactions, automatic scaling and load balancing, APIs for authenticating users and sending email using Google Accounts, and a fully featured local development environment. Project Hosting on Google Code is a free service to the open source community. Easy to build, Easy to scale, Easy to maintain * Zero to sixty: Scale your app automatically without worrying about managing machines. * Supercharged APIs: Supercharge your app with services such as Task Queue, XMPP, and Cloud SQL, all powered by the same infrastructure that powers the Google services you use every day. * You''re in control: Manage your application with a simple, web-based dashboard allowing you to customize your app''s performance. | email, environment, application, code, google, storage, technology, web, java, python, go, plugin, eclipse, php | is listed by: OMICtools | Free, Up to 1 GB of storage, Pay for resources above the free levels | nif-0000-10240, OMICS_01211 | http://code.google.com/appengine/ | SCR_006496 | Google App Engine: Platform as a Service, Google App Engine - Google Developers | 2026-08-08 12:04:59 | 1 | ||||||
|
HTQC Resource Report Resource Website 10+ mentions |
HTQC (RRID:SCR_006448) | HTQC | software resource, software toolkit | A software toolkit including statistics tool for illumina high-throughput sequencing data, and filtration tools for sequence quality, length, tail quality, etc.. | c++, illumina, command-line |
is listed by: OMICtools is listed by: Debian has parent organization: SourceForge |
PMID:23363224 DOI:10.1186/1471-2105-14-33 |
GNU General Public License, v3 | OMICS_01052 | https://sources.debian.org/src/htqc/ | SCR_006448 | HTQC - Quality control and filtration for illumina sequencing data | 2026-08-08 12:04:49 | 43 | |||||
|
Mash Resource Report Resource Website 50+ mentions |
Mash (RRID:SCR_019135) | software resource, data analytics software, software application | Software tool for genome and metagenome distance estimation using MinHash. Reduces large sequences and sequence sets to small, representative sketches, from which global mutation distances can be rapidly estimated. | Genome distance estimation, metagenome distance estimation, MinHash, mutation distance, sequence, sequence set |
is listed by: Debian is listed by: OMICtools |
NHGRI ; NIH |
PMID:27323842 | Free, Available for download, Freely available | OMICS_10468 | https://mash.readthedocs.io/en/latest/, https://sources.debian.org/src/mash/ | SCR_019135 | 2026-08-08 12:05:25 | 75 | ||||||
|
Scoary Resource Report Resource Website 10+ mentions |
Scoary (RRID:SCR_021087) | software resource, data analytics software, software application | Software tool that scores components of pan genome for associations to observed phenotypic traits while accounting for population stratification, with minimal assumptions about evolutionary processes.Designed to take gene presence absence.csv file from Roary as well as traits file created by user and calculate associations between all genes in accessory genome and traits. It reports list of genes sorted by strength of association per trait. | Gene associations calculation, accessory genome, phenotypic traits, gene presence, gene absence, gene sort, association strenght |
is listed by: Debian is listed by: OMICtools works with: Roary |
Norwegian Institute of Public Health ; Norwegian Research Council |
PMID:27887642 | Free, Available for download, Freely available | OMICS_13120 | https://sources.debian.org/src/scoary/ | SCR_021087 | 2026-08-08 12:05:26 | 20 | ||||||
|
Duplicate reads removal Resource Report Resource Website |
Duplicate reads removal (RRID:SCR_000231) | Duplicate reads removal | commercial organization, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Plug-in tool to filter out duplicate reads that is specifically well-suited to handle those coming from PCR amplification errors which can have a negative effect because a certain sequence is represented in artificially high numbers. | pcr amplification, duplicate, read | is listed by: OMICtools | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02101 | SCR_000231 | 2026-08-08 12:05:43 | 0 | ||||||||
|
Lab7 Resource Report Resource Website |
Lab7 (RRID:SCR_001210) | Lab7 | commercial organization, software resource | Software to address all aspects of Next Generation Sequencing data workflow. | next-generation sequencing | is listed by: OMICtools | Commerical | OMICS_02132 | SCR_001210 | Lab7 Systems | 2026-08-08 12:05:45 | 0 | |||||||
|
Omixon Target HLA Typing Resource Report Resource Website 1+ mentions |
Omixon Target HLA Typing (RRID:SCR_001206) | Omixon Target HLA | commercial organization, software resource | An optional module in the Omixon Target application suite for HLA typing using NGS (next-generation sequencing) data that gives high resolution results with whole genome, exome or very targeted DNA data, or with RNA seq data. | whole genome, exome, target dna, rna-seq, hla allele, hla, allele, next-generation sequencing |
is listed by: OMICtools has parent organization: Omixon Target Data Analysis |
License required | OMICS_02142 | SCR_001206 | 2026-08-08 12:05:39 | 1 | ||||||||
|
SNP and Variation Suite SNP Analysis Resource Report Resource Website 1+ mentions |
SNP and Variation Suite SNP Analysis (RRID:SCR_001285) | SVS SNP Analysis | software resource | SNP Analysis software for basic to advanced analyses that incorporates a number of intuitive workflows to lead you beyond single marker associations. With support for case-control and quantitative traits, whole genome and candidate gene data, you can run a breadth of statistical tests under several genetic models. Advanced regression can further help elucidate even the most complex gene-gene and gene-environment interactions. | single nucleotide polymorphism, linkage disequilibrium, haplotype, homozygosity |
is listed by: OMICtools has parent organization: Golden Helix Incorporated |
Restricted | OMICS_02052 | SCR_001285 | SNP and Variation Suite: SNP Analysis, SNP Package of SVS 7, SNP & Variation Suite (SVS) SNP Analysis, SNP & Variation Suite SNP Analysis, SNP & Variation Suite: SNP Analysis | 2026-08-08 12:05:46 | 1 | |||||||
|
VectorFriends Resource Report Resource Website |
VectorFriends (RRID:SCR_001230) | VectorFriends | commercial organization, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 18,2025. Sequence analysis software for molecular biologists. | cloning, isothermal assembly, pcr, primer design, data management, sequence analysis, sequence, analysis, primer, windows, mac os | is listed by: OMICtools | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02113 | SCR_001230 | 2026-08-08 12:05:39 | 0 | ||||||||
|
Anchored Assembly Resource Report Resource Website |
Anchored Assembly (RRID:SCR_001188) | Anchored Assembly | commercial organization, software resource | Analysis pipeline that accurately detects and maps variations that are often missed by standard analysis algorithms. It uses direct de novo read overlap assembly to accurately detect and characterize SNPs (single nucleotide polymorphisms), indels, and SVs (structural variations). The pipeline uses existing Illumina HiSeq data and does not require additional library preparation. The algorithm is optimized for projects with at least 20x coverage per chromosome set (i.e. 40x for diploid). | variation, structural variation, single nucleotide polymorphism |
is listed by: OMICtools has parent organization: Spiral Genetics Incorporated |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02167 | SCR_001188 | 2026-08-08 12:05:45 | 0 | ||||||||
|
OmicsOffice for NGS SeqSolve Resource Report Resource Website |
OmicsOffice for NGS SeqSolve (RRID:SCR_001222) | OmicsOffice for NGS | commercial organization, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 18,2025. Software for secondary and tertiary analysis of Next Generation Sequencing (NGS) data. | next-generation sequencing, rna-seq, chip-seq, transcript, alternative splicing, variant, mirna, non-coding rna expression, genome, differential expression, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:20671709 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:seqsolve, OMICS_02111 | https://bio.tools/seqsolve | SCR_001222 | OmicsOffice for NGS (SeqSolve), SeqSolve | 2026-08-08 12:05:45 | 0 | |||||
|
Methyl-Analyzer Resource Report Resource Website |
Methyl-Analyzer (RRID:SCR_000318) | software resource, source code | A data analysis pipeline for the Methyl-MAPS method. | methyl maps, data analysis, python, pipeline | is listed by: OMICtools | PMID:21685051 | Free, Available for download, Freely available | OMICS_00617 | SCR_000318 | 2026-08-08 12:05:37 | 0 |
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