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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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ArtificialFastqGenerator Resource Report Resource Website 10+ mentions |
ArtificialFastqGenerator (RRID:SCR_006880) | ArtificialFastqGenerator | software resource | Software to evaluate and improve the accuracy of sequencing error under different experimental conditions. It can identify which components of a system may be suboptimal and which regions of the genome may be problematic. | matlab, java, Next Generation Sequencing, aligns reads, reference genome |
is listed by: OMICtools is listed by: Debian |
PMID:23152858 | GNU GPL v3 | OMICS_00248, SCR_015979 | https://sources.debian.org/src/artfastqgenerator/ | SCR_006880 | Artfastqgenerator - Ouputs artificial FASTQ files derived from a reference genome | 2026-02-14 02:01:24 | 10 | |||||
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BarraCUDA Resource Report Resource Website 1+ mentions |
BarraCUDA (RRID:SCR_006881) | BarraCUDA | software resource | A sequence mapping software that utilizes the massive parallelism of graphics processing units to accelerate the inexact alignment of short sequence reads to a particular location on a reference genome. It can align a paired-end library containing 14 million pairs of 76bp reads to the Human genome in about 27 minutes (from fastq files to SAM alignment) using a ��380 NVIDIA Geforce GTX 680*. The alignment throughput can be boosted further by using multiple GPUs (up to 8) at the same time. Being based on BWA (http://bio-bwa.sf.net) from the Sanger Institute, BarraCUDA delivers a high level of alignment fidelity and is comparable to other mainstream alignment programs. It can perform gapped alignment with gap extensions, in order to minimise the number of false variant calls in re-sequencing studies. | gpu/cuda, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Cambridge; Cambridge; United Kingdom has parent organization: SourceForge |
PMID:22244497 PMID:19451168 |
Acknowledgement requested | OMICS_00650, biotools:barracuda | https://bio.tools/barracuda | SCR_006881 | 2026-02-14 02:01:17 | 4 | ||||||
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CROP Resource Report Resource Website 100+ mentions |
CROP (RRID:SCR_006916) | CROP | software resource | A clustering tool designed mainly for Metagenomics studies, which clusters 16S rRNA sequences into Operational Taxonomic Units (OTU). By using a Gaussian Mixture model, CROP can automatically determine the best clustering result for 16S rRNA sequences at different phylogenetic levels without setting a hard cutoff threshold as hierarchical clustering does. Yet, at the same time, it is able to manage large datasets and to overcome sequencing errors. | cluster, 16s rrna, otu, gaussian mixture, bayesian, mcmc, metagenomics |
is listed by: OMICtools has parent organization: Google Code has parent organization: University of Southern California; Los Angeles; USA |
PMID:21233169 | OMICS_01442 | SCR_006916 | CROP: Clustering 16S rRNA For OTU Prediction | 2026-02-14 02:01:25 | 204 | |||||||
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Stanley Medical Research Institute Resource Report Resource Website 1+ mentions |
Stanley Medical Research Institute (RRID:SCR_007047) | SMRI | institution | The Stanley Medical Research Institute (SMRI) is a nonprofit organization supporting research on the causes of, and treatments for, schizophrenia and bipolar disorder. Since it began in 1989, SMRI has supported more than $300 million in research in over 30 countries around the world. It is the largest nongovernmental source of funds for research on these diseases in the United States. Schizophrenia and bipolar disorder are the most important psychiatric disorders in the United States, affecting more than 4 million people at any given time. Until recent years, little research had been done on these diseases, and the treatment of them was unsatisfactory. The neuroscience revolution has brought with it great opportunities for increased understanding of brain diseases such as schizophrenia and bipolar disorder. SMRI is on the leading edge of this exciting research. Approximately 75 percent of SMRI expenditures goes towards the development of new treatments for schizophrenia and bipolar disorder. The remaining funds are used for research on the causes of these diseases. SMRI has a close relationship with and is the supporting organization for the Treatment Advocacy Center (TAC). The Treatment Advocacy Center is a nonprofit organization dedicated to eliminating barriers to the timely and effective treatment of severe psychiatric disorders. TAC promotes laws, policies, and practices for the delivery of psychiatric care and supports the development of innovative treatments for and research into the causes of severe and persistent psychiatric disorders, such as schizophrenia and bipolar disorder. | schizophrenia, bipolar disorder, major depressive disorder, depressive disorder, mental disease |
is parent organization of: Stanley Neuropathology Consortium Integrative Database is parent organization of: Stanley Medical Research Institute Online Genomics Database is parent organization of: Stanley Brain Collection |
grid.453353.7, Crossref funder ID: 100007123, nlx_143934, ISNI: 0000 0004 0473 2858 | https://ror.org/01pj5nn22 | SCR_007047 | 2026-02-14 02:01:17 | 1 | ||||||||
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Diabetes Autoantibody Standardization Program Resource Report Resource Website 10+ mentions |
Diabetes Autoantibody Standardization Program (RRID:SCR_006929) | DASP | knowledge environment | Program that develops materials and methods to improve measurements of autoantibodies that are predictive of type 1 diabetes. These are the most sensitive and meaningful measures for predicting this disease. Historically, autoantibody measures have been variable among laboratories; therefore, this program, in collaboration with the Immunology of Diabetes Society, was established. The goals of DASP are to improve laboratory methods, evaluate laboratory performance, support the development of sensitive and specific measurement technologies, and develop reference methods. Currently, 48 key laboratories from 19 countries participate in DASP. | autoantibody, quality assurance, standardization, standard, laboratory method, laboratory performance, measurement, method |
is related to: NIDDK Information Network (dkNET) has parent organization: Centers for Disease Control and Prevention |
Type 1 diabetes, Diabetes | PMID:12716742 | nlx_152868 | http://www.idsoc.org/committees/antibody/dasphome.html | SCR_006929 | Diabetes Autoantibody Standardization Program (DASP) | 2026-02-14 02:01:24 | 14 | |||||
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MetMap Resource Report Resource Website 1+ mentions |
MetMap (RRID:SCR_006954) | MetMap | software resource | A computational pipeline for the analysis of MethylSeq experiments., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. |
is listed by: OMICtools has parent organization: University of California at Berkeley; Berkeley; USA |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00618 | SCR_006954 | 2026-02-14 02:01:26 | 9 | |||||||||
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Myrna Resource Report Resource Website 1+ mentions |
Myrna (RRID:SCR_006951) | Myrna | software resource | A cloud computing tool for calculating differential gene expression in large RNA-seq datasets. It uses Bowtie for short read alignment and R/Bioconductor for interval calculations, normalization, and statistical testing. These tools are combined in an automatic, parallel pipeline that runs in the cloud (Elastic MapReduce in this case) on a local Hadoop cluster, or on a single computer, exploiting multiple computers and CPUs wherever possible. | mapreduce, hadoop, cloud computing, differential expression, gene expression, rna-seq, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: ReCount - A multi-experiment resource of analysis-ready RNA-seq gene count datasets has parent organization: Johns Hopkins University; Maryland; USA |
PMID:20701754 | Artistic License | OMICS_01310, biotools:myrna | https://github.com/BenLangmead/myrna https://bio.tools/myrna |
SCR_006951 | Myrna: Cloud-scale differential gene expression for RNA-seq | 2026-02-14 02:01:18 | 2 | |||||
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Australian Government Bureau of Meteorology Resource Report Resource Website 100+ mentions |
Australian Government Bureau of Meteorology (RRID:SCR_007158) | AU BOM | nonprofit organization | The Bureau of Meteorology is Australia''s national weather, climate and water agency. Its expertise and services assist Australians in dealing with the harsh realities of their natural environment, including drought, floods, fires, storms, tsunami and tropical cyclones. Through regular forecasts, warnings, monitoring and advice spanning the Australian region and Antarctic territory, the Bureau provides one of the most fundamental and widely used services of government. The Bureau contributes to national social, economic, cultural and environmental goals by providing observational, meteorological, hydrological and oceanographic services and by undertaking research into science and environment related issues in support of its operations and services. The Bureau of Meteorology operates under the authority of the Meteorology Act 1955 and the Water Act 2007 which provide the legal basis for its activities, while its operation is continually assessed in accordance with the national need for climatic records, water information, scientific understanding of Australian weather and climate and effective service provision to the Australian community. The Bureau of Meteorology must also fulfill Australia''s international obligations under the Convention of the World Meteorological Organization (WMO) and related international meteorological treaties and agreements. | meteorology, weather, climate, water, natural, environment, flood, fire, strom, tsunami, tropical, cyclone, economic, social, cultural, environmental, oceanographic, research, science, environment | Commonwealth of Australia | nif-0000-30228, ISNI: 000000011086859X, grid.1527.1, Wikidata: Q923429 | https://ror.org/04dkp1p98 | SCR_007158 | AU BOM | 2026-02-14 02:01:27 | 159 | |||||||
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Swami: The Next Generation Biology Workbench Resource Report Resource Website 1+ mentions |
Swami: The Next Generation Biology Workbench (RRID:SCR_007217) | NGBW | service resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. The Next Generation Biology Workbench is a free resource for research and education in Bioinformatics, Genomics, Proteomics, and Phylogenetics. The NGBW is a re-engineering of the Biology Workbench which was designed by Shankar Subramaniam and his group to provide an integrated environment where tools, user data, and public data resources can be easily accessed. The NGBW is designed to be an organic tool that evolves with the needs of the Biomedical research and education communities. The Next Generation Biology Workbench (NGBW) is now available for public use, in its production release. | has parent organization: University of California at San Diego; California; USA | IBM Corporation ; Microsoft Research ; NIGMS 5R01GM073931 |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_14257 | http://www.ngbw.org/ | SCR_007217 | Next Generation Biology Workbench, Swami | 2026-02-14 02:01:19 | 2 | ||||||
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Cerrado concepts and plant community dynamics Resource Report Resource Website 1+ mentions |
Cerrado concepts and plant community dynamics (RRID:SCR_007174) | CCON | data or information resource, ontology, controlled vocabulary | Ontology of Cerrado wood plant dynamics to represent the set of concepts about the dynamics, that is, changes over time of the wood vegetation structure, of Cerrado. Ccon describes the main parameters used to measure the changes, such as mortality rate and recruitment rate. | owl | is listed by: BioPortal | nlx_157361 | SCR_007174 | 2026-02-14 02:01:27 | 2 | |||||||||
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GRAPPA: Genome Rearrangements Analysis under Parsimony and other Phylogenetic Algorithms Resource Report Resource Website 10+ mentions |
GRAPPA: Genome Rearrangements Analysis under Parsimony and other Phylogenetic Algorithms (RRID:SCR_007208) | GRAPPA | software resource | As fascinating as diversity is, it''s not the sort of thing that computational scientists usually get excited about. Uncovering how diversity came to be has captured the attention of a team of researchers at Alliance partner University of New Mexico and the University of Texas, though. Using the 512-processor LosLobos Linux Pentium III supercomputing cluster at the Albuquerque High Performance Computing Center, the team has created a phylogeny reconstruction - or evolutionary history - of 12 bluebell species, predicting all of the steps that take these species back to a single common ancestor. To meet the challenge, they created a whole new piece of software known as GRAPPA. GRAPPA is is free software available as a gzipped tar file containing all source files needed to compile an executable version. | has parent organization: University of New Mexico; New Mexico; USA | PMID:11262975 | nlx_27473 | SCR_007208 | 2026-02-14 02:01:28 | 27 | |||||||||
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Broad Institute Resource Report Resource Website 1000+ mentions |
Broad Institute (RRID:SCR_007073) | Broad | institution | Biomedical and genomic research center located in Cambridge, Massachusetts, United States. Nonprofit research organization under the name Broad Institute Inc., and is partners with Massachusetts Institute of Technology, Harvard University, and the five Harvard teaching hospitals. Dedicated to advance understanding of biology and treatment of human disease to improve human health. | biomedical, genomic, research, center, nonprofit, organization, human, biology, disease |
is affiliated with: Massachusetts Institute of Technology; Massachusetts; USA; is affiliated with: Harvard University; Cambridge; United States is affiliated with: Integrative Human Microbiome Project is affiliated with: MIT; Cambridge; Massachusetts; United States is related to: LINCS Information Framework is related to: HMS LINCS Database is related to: Cancer Cell Line Encyclopedia is related to: GO2MSIG is parent organization of: ARACHNE is parent organization of: MuTect is parent organization of: SiPhy is parent organization of: ContEst is parent organization of: Broad Minded is parent organization of: JBrowse is parent organization of: Birdseed is parent organization of: VAAL is parent organization of: SomaticCall is parent organization of: BIRDSUITE is parent organization of: GATK is parent organization of: SNAP - SNP Annotation and Proxy Search is parent organization of: SYZYGY is parent organization of: Genetic Maps of the Rat Genome is parent organization of: LINCS Connectivity Map is parent organization of: Classification of Human Lung Carcinomas by mRNA Expression Profiling Reveals Distinct Adenocarcinoma Sub-classes is parent organization of: Haploview is parent organization of: Magnaporthe comparative Database is parent organization of: GeneCruiser is parent organization of: Fungal Genome Initiative is parent organization of: Gene Set Enrichment Analysis is parent organization of: GenePattern is parent organization of: MAGENTA is parent organization of: Multiple Myeloma Genomics Portal is parent organization of: ExAc is parent organization of: Ricopili is parent organization of: UnifiedGenotyper is parent organization of: SomaticIndelDetector is parent organization of: RNA-SeQC is parent organization of: Oncotator is parent organization of: ABSOLUTE is parent organization of: PathSeq is parent organization of: V-Phaser 2 is parent organization of: Indelocator is parent organization of: Scripture is parent organization of: VICUNA is parent organization of: Tuberculosis Database is parent organization of: HaploReg is parent organization of: CellProfiler Image Analysis Software is parent organization of: National Institute of Mental Health (NIMH) Human Genetics Initiative is parent organization of: ChemBank is parent organization of: GeneCluster 2: An Advanced Toolset for Bioarray Analysis is parent organization of: Ultrasome is parent organization of: Diabetes Genetics Initiative is parent organization of: Dog Genome Project is parent organization of: Gene Relationships Across Implicated Loci is parent organization of: InVEx is parent organization of: Broad Genetic Analysis Platform is parent organization of: CellProfiler Analyst is parent organization of: ALLPATHS-LG is parent organization of: MutSig is parent organization of: SegSeq is parent organization of: Argo Genome Browser is parent organization of: Integrative Genomics Viewer is parent organization of: MEDEA is parent organization of: Pathline is parent organization of: ASPGD is parent organization of: DGAP is parent organization of: BARD is parent organization of: 1000 Genomes: A Deep Catalog of Human Genetic Variation is parent organization of: Trinity is parent organization of: Genome Aggregation Database is parent organization of: GenomeSpace is parent organization of: Picard is parent organization of: Connectivity Map 02 is parent organization of: CMap is parent organization of: IndelGenotyper is parent organization of: Discovar assembler is parent organization of: Molecular Signatures Database is parent organization of: GSEA is parent organization of: Eagle is parent organization of: Morpheus by Broad Institute is parent organization of: Cancer Dependency Map Portal is parent organization of: LIGER is parent organization of: Drop-seq tools is parent organization of: scATAC Pipeline is parent organization of: Guide Design Resources is parent organization of: Smart-seq2 Single Sample Pipeline is parent organization of: Smart-seq2 Single Nucleus Multi Sample Pipeline is parent organization of: Broad Terra cloud commons for pathogen surveillance is parent organization of: Single Cell Portal is parent organization of: CEMBA MethylC Seq Pipeline is parent organization of: Pegasus is parent organization of: Cumulus is parent organization of: Cirrocumulus is parent organization of: BICCN Anatomy and Morphology Project is parent organization of: Terra is parent organization of: JUMP Cell Painting Consortium is parent organization of: Spectrum Mill is parent organization of: Polysolver is parent organization of: Brain Cell Data Viewer is parent organization of: Eagle is parent organization of: Broad Institute Imaging Platform Core Facility is parent organization of: ATAC Pipeline is parent organization of: ichorCNA is parent organization of: CRISPick is parent organization of: FireBrowse is parent organization of: Cellarium is parent organization of: multiVIB is parent organization of: SlideTags.wdl is parent organization of: Slide-seq Pipeline is parent organization of: BuildIndices |
Eli and Edythe Broad ; individual donors |
nif-0000-31438, grid.66859.34, Wikidata: Q4971893 | https://ror.org/05a0ya142 | SCR_007073 | Broad Institute of MIT and Harvard, Broad Institute Inc. | 2026-02-14 02:01:20 | 1897 | ||||||
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University of Reading; Reading; United Kingdom Resource Report Resource Website 1+ mentions |
University of Reading; Reading; United Kingdom (RRID:SCR_007135) | university | Public university in Reading, Berkshire, England. It was founded in 1892 as University College, Reading, a University of Oxford extension college. |
is parent organization of: Catalogue of Life is parent organization of: neuroade is parent organization of: Species 2000 is parent organization of: Neuromantic |
Crossref funder ID:501100000839, Wikidata:Q1432632, ISNI:0000 0004 0457 9566, grid.9435.b, nlx_99449 | https://ror.org/05v62cm79 | SCR_007135 | 2026-02-14 02:01:27 | 6 | ||||||||||
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Cell Culture Ontology Resource Report Resource Website 1+ mentions |
Cell Culture Ontology (RRID:SCR_007096) | CCONT | data or information resource, ontology, controlled vocabulary | ontology for the formal representation of cell lines and their correspnding culture conditions. | owl | is listed by: BioPortal | nlx_157354 | SCR_007096 | 2026-02-14 02:01:26 | 1 | |||||||||
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swDMR Resource Report Resource Website 10+ mentions |
swDMR (RRID:SCR_007316) | swDMR | software resource | A free software using a sliding-window approach to identify differentially methylated regions (DMR) from whole-genome bisulfite sequencing. |
is listed by: OMICtools has parent organization: Google Code |
Apache License | OMICS_00625 | SCR_007316 | 2026-02-14 02:01:30 | 23 | |||||||||
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GEB Resource Report Resource Website 1+ mentions |
GEB (RRID:SCR_007395) | GEB | software resource | A Java application developed to visualise distribution of genomic features in high resolution. | is listed by: OMICtools | OMICS_00911 | SCR_007395 | Genome Environment Browser | 2026-02-14 02:01:25 | 2 | |||||||||
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Biological General Repository for Interaction Datasets (BioGRID) Resource Report Resource Website 1000+ mentions |
Biological General Repository for Interaction Datasets (BioGRID) (RRID:SCR_007393) | BioGRID | data or information resource, database | Curated protein-protein and genetic interaction repository of raw protein and genetic interactions from major model organism species, with data compiled through comprehensive curation efforts. | budding yeast, fission yeast, protein, gene, protein interaction, genetic interaction, model organism, interaction, dataset, gene annotation, phenotype, orthologous interaction, yeast, cellular interaction network, physical interaction, protein-peptide, protein-rna, protein-protein interaction, genetics, publication, raw protein, genetic interaction, web service, pathway, network, biology, gene mapping, statistics, bio.tools, FASEB list |
is used by: NIF Data Federation is recommended by: National Library of Medicine is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: re3data.org is listed by: OMICtools is listed by: DataCite is listed by: NIH Data Sharing Repositories is listed by: bio.tools is listed by: Debian is related to: TissueNet - The Database of Human Tissue Protein-Protein Interactions is related to: Pathway Commons is related to: Cytoscape is related to: Interaction Reference Index is related to: ConsensusPathDB is related to: FlyMine is related to: IMEx - The International Molecular Exchange Consortium is related to: Integrated Molecular Interaction Database is related to: PSICQUIC Registry is related to: PSI-MI is related to: NIH Data Sharing Repositories is related to: Agile Protein Interactomes DataServer is related to: Integrated Manually Extracted Annotation has parent organization: Princeton University; New Jersey; USA has parent organization: University of Edinburgh; Scotland; United Kingdom has parent organization: University of Montreal; Quebec; Canada works with: IMEx - The International Molecular Exchange Consortium |
NCRR R01 RR024031; NHGRI HG02223; Canadian Institutes of Health Research ; BBSRC ; NIH Office of the Director R24 OD011194 |
PMID:23203989 PMID:21071413 PMID:16381927 PMID:12620108 |
Free, Freely available | nif-0000-00432, r3d100010350, OMICS_01901, biotools:the_grid | https://orip.nih.gov/comparative-medicine/programs/genetic-biological-and-information-resources https://bio.tools/the_grid https://doi.org/10.17616/R34C7G |
SCR_007393 | , BioGRID, Biological General Repository for Interaction Datasets | 2026-02-14 02:01:30 | 2554 | ||||
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FlexProt: flexible protein alignment Resource Report Resource Website 1+ mentions |
FlexProt: flexible protein alignment (RRID:SCR_007306) | software resource | FlexProt detects the optimal flexible structural alignment of a pair of protein structures. The first structure is assumed to be rigid, while in the second structure potential flexible regions are automatically detected. | bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Tel Aviv University; Ramat Aviv; Israel |
nif-0000-00159, biotools:flexprot | https://bio.tools/flexprot | SCR_007306 | FlexPROT | 2026-02-14 02:01:29 | 1 | ||||||||
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Neurotree: Academic Family Tree Resource Report Resource Website 1+ mentions |
Neurotree: Academic Family Tree (RRID:SCR_007383) | people resource | An academic genealogy platform that collects information about graduate students and posdoctoral research connections. The Neuroscience Academic Family Tree is a free, volunteer-run website designed to help you track your academic genealogy. Our goal is to collect information about the graduate student and postdoctoral connections between most researchers in the field. :How do I navigate the tree? :There are several ways to wander around Neurotree. The basics are summed up in the commands at the top of each page: :* Tree - Jump to a random node on the tree :* Search - Search for a specific person or people at a specific institution :* Recent additions - List the most recent additions :* Distance - Trace the connection between two people in the tree :* Add person - Add a new person to the tree (and be a good citizen!). You must sign up for an account to make additions. :* Analysis - Learn more amazing facts about neurogenealogy! ... and possibly something about the field of neuroscience. | database | PMID:23071595 | nif-0000-00383 | SCR_007383 | Neurotree | 2026-02-14 02:01:30 | 1 | |||||||||
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Taipan Resource Report Resource Website 1+ mentions |
Taipan (RRID:SCR_007330) | Taipan | software resource | A fast hybrid short-read assembly tool. | c, unix/linux, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:19535537 | GNU General Public License, v2 | OMICS_00035, biotools:taipan | https://bio.tools/taipan | SCR_007330 | 2026-02-14 02:01:29 | 2 |
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