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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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ContEst Resource Report Resource Website 1+ mentions |
ContEst (RRID:SCR_000595) | ContEst | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 8,2025. A software tool (and method) for estimating the amount of cross-sample contamination in next generation sequencing data. | java, contamination, next-generation sequencing, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Broad Institute |
PMID:21803805 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01038, biotools:contest | https://bio.tools/contest | SCR_000595 | 2026-02-07 02:05:23 | 5 | ||||||
|
BLASR Resource Report Resource Website 10+ mentions Discontinued |
BLASR (RRID:SCR_000764) | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. C++ long-read aligner for PacBio reads., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | standalone software, c++, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: Proovread |
PMID:22988817 DOI:10.1186/1471-2105-13-23 |
THIS RESOURCE IS NO LONGER IN SERVICE | biotools:blasr, OMICS_05134 | https://bio.tools/blasr https://sources.debian.org/src/blasr/ |
SCR_000764 | Basic Local Alignment with Successive Refinement, BLASR: The PacBio long read aligner | 2026-02-07 02:05:23 | 15 | ||||||
|
GMcloser Resource Report Resource Website 1+ mentions |
GMcloser (RRID:SCR_000646) | GMcloser | software resource | Software that fills and closes the gaps present in scaffold assemblies, especially those generated by the de novo assembly of whole genomes with next-generation sequencing (NGS) reads. Unlike other gap-closing tools that use only NGS reads, GMcloser uses preassembled contig sets or long read sets as the sequences to close gaps and uses paired-end (PE) reads and a likelihood-based algorithm to improve the accuracy and efficiency of gap closure. The efficiency of gap closure can be increased by successive treatments with different contig sets. | scaffolding, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:26261222 | Free, Available for download, Freely available | biotools:gmcloser, OMICS_00042 | https://bio.tools/gmcloser | SCR_000646 | Gmcloser - Closing the gaps in scaffolds with preassembled contigs | 2026-02-07 02:05:25 | 3 | |||||
|
FastUniq Resource Report Resource Website 1+ mentions |
FastUniq (RRID:SCR_000682) | software resource | A software tool for removal of de novo duplicates in paired short DNA sequences. | de novo, dna, sequence, duplicate, |
is listed by: OMICtools has parent organization: SourceForge |
DOI:10.1371/journal.pone.0052249 | Free, Available for download, Freely available | OMICS_01044 | SCR_000682 | 2026-02-07 02:05:25 | 3 | ||||||||
|
Sequencing Analysis Software Resource Report Resource Website 1+ mentions |
Sequencing Analysis Software (RRID:SCR_000718) | Sequencing Analysis Software | software resource | A software that gives the user the ability to basecall, trim, display, edit, and print data for the entire line of capillary DNA sequencing instruments for data analysis and quality control. This software benefits from being able to obtain longer read lengths, greater accuracy on the 5' end, and the ability to filter out low-quality sequence ends. | basecall, capillary dna, quality control, low-quality sequence ends | is listed by: OMICtools | Restricted | OMICS_01814 | SCR_000718 | 2026-02-07 02:05:26 | 1 | ||||||||
|
NGS tools for the novice Resource Report Resource Website 1+ mentions |
NGS tools for the novice (RRID:SCR_000664) | NGS tools for the novice | software resource | A collection of simple Perl scripts adressed to scientists doing research that bases on high throughput genomic/transcriptomic data. It does not require any bioinformatic expertise. The scripts perform fundamental processing steps like sorting sequences by TAGs, FASTQ to FASTA conversion, filtering and counting of redundant sequences, individually adjustable FASTQ quality filtering or basic analyses like base count and analysis of sequence length distribution. | next generation sequencing, perl |
is listed by: OMICtools has parent organization: SourceForge |
Free, Available for download, Freely available | OMICS_01063 | SCR_000664 | NGS tools for the novice - Handy tools for processing of next generation sequencing (NGS) data | 2026-02-07 02:05:22 | 3 | |||||||
|
Opera Resource Report Resource Website 1+ mentions |
Opera (RRID:SCR_000665) | software resource | A sequence assembly software program that uses information from paired-end reads to optimally order and orient contigs assembled from shotgun-sequencing reads. | sequence assembly, paired-end, orient contigs, shotgun-sequencing, shotgun, software program, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:27169502 PMID:21929371 |
Free, Available for download, Freely available | biotools:opera, OMICS_00045 | https://bio.tools/opera | SCR_000665 | OPERA-LG, Optimal Paired-End Read Assembler | 2026-02-07 02:05:24 | 3 | ||||||
|
RMAP Resource Report Resource Website 1+ mentions |
RMAP (RRID:SCR_000695) | RMAP | software resource | Software for short-read mapping to accurately map reads from the next-generation sequencing technology. It can map reads with or without error probability information (quality scores) and supports paired-end reads or bisulfite-treated reads mapping. There is no limitaions on read widths or number of mismatches. RMAP can now map more than 8 million reads in an hour at full sensitivity to 2 mismatches. | next-generation sequencing, solexa |
is listed by: OMICtools has parent organization: Cold Spring Harbor Laboratory |
PMID:19736251 | OMICS_00681 | SCR_000695 | 2026-02-07 02:05:26 | 2 | ||||||||
|
TMAP Resource Report Resource Website 10+ mentions |
TMAP (RRID:SCR_000687) | TMAP | software resource | Alignment software for short and long nucleotide sequences produced by next-generation sequencing technologies. | next-generation sequencing | is listed by: OMICtools | Free, Available for download, Freely available | OMICS_00694 | SCR_000687 | TMAP - torrent mapping alignment program, Torrent Mapping Alignment Program | 2026-02-07 02:05:22 | 22 | |||||||
|
Frontier Scientific Chemical Supplier Resource Report Resource Website 10+ mentions |
Frontier Scientific Chemical Supplier (RRID:SCR_000914) | commercial organization | A commercial vendor of chemicals that provides custom synthesis of a wide variety of organic compounds. Frontier Scientific has capabilities for custom work in organoborons, organotins, porphyrins, silanes, halogenations, catalysts and cross couplings using Suzuki, Stille, and Kumada processes. | organoborons, organotins, porphyrins, silanes, halogenations, catalysts, cross couplings, chemical, organic, compound, custom, synthesize | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_157824, grid.504592.f | https://ror.org/00d403277 | http://frontiersci.com/ | SCR_000914 | 2026-02-07 02:05:26 | 24 | ||||||||
|
University of Dundee; Scotland; United Kingdom Resource Report Resource Website 1+ mentions |
University of Dundee; Scotland; United Kingdom (RRID:SCR_000997) | university | University in Scotland, UK that provides undergraduate and doctoral degree programs. | university, undergraduate, doctoral, phd, graduate |
is related to: Kinetics for Drug Discovery is related to: Aline is parent organization of: Phospho.ELM is parent organization of: MARCAR is parent organization of: OXBench is parent organization of: GOtcha is parent organization of: Jalview is parent organization of: Kinomer is parent organization of: Human Intermediate Filament Database is parent organization of: SNAPPI is parent organization of: OME - Open Microscopy Environment is parent organization of: University of Dundee College of Life Sciences; Scotland; United Kingdom is parent organization of: University of Dundee School of Medicine; Scotland; United Kingdom is parent organization of: NoPdb: Nucleolar Proteome Database is parent organization of: Research Data Management Platform |
Crossref funder ID:100008890, ISNI:0000 0004 0397 2876, grid.8241.f, Wikidata:Q1249005, nlx_76402 | https://ror.org/03h2bxq36 | SCR_000997 | University of Dundee | 2026-02-07 02:05:26 | 2 | ||||||||
|
Tufts University; Massachusetts; USA Resource Report Resource Website 1+ mentions |
Tufts University; Massachusetts; USA (RRID:SCR_000994) | university | Private research university in Medford and Somerville, Massachusetts, United States, with additional facilities in Boston and Grafton, as well as Talloires, France. Provides undergraduate, graduate, and professional degree programs. | tufts, university, undergraduate, graduate, professional |
uses: LabArchives is related to: Clinical and Translational Science Awards Consortium is related to: LabArchives is parent organization of: Tissue Engineering Resource Center is parent organization of: Tufts University School of Medicine; Massachusetts; USA is parent organization of: Tufts University Graduate School of Biomedical Sciences Graduate Programs is parent organization of: DFLAT is parent organization of: Tufts University Labs and Facilities is parent organization of: Tufts University Core Facilities is parent organization of: FluCalc is parent organization of: Tufts University Genomics Core Facility is parent organization of: Tufts University Laser Cytometry Core Facility |
Crossref funder ID:100008090, ISNI:0000 0004 1936 7531, Wikidata:Q49120, nlx_38314, grid.429997.8 | https://ror.org/05wvpxv85 | SCR_000994 | Tufts University, Tufts | 2026-02-07 02:05:26 | 9 | ||||||||
|
Pasteur Institute of Lille; Lille; France Resource Report Resource Website 1+ mentions |
Pasteur Institute of Lille; Lille; France (RRID:SCR_000990) | institution | Pasteur Institute of Lille is an international research institute in Lille, France focused on bettering human health by detecting risk factors in degenerative diseases. | institute, france research, international research, lille research, human health, degenerative disease, risk factor |
is related to: AgedBrainSYSBIO is related to: International Genomics of Alzheimers Project has parent organization: Pasteur Institute is parent organization of: International Genomics of Alzheimers Project |
grid.8970.6, nlx_158125, ISNI: 0000 0001 2159 9858, Wikidata: Q3151788 | https://ror.org/05k9skc85 | SCR_000990 | Pasteur Institute of Lille, Pasteur Lille, Pasteur-Lille, Institut Pasteur de Lille | 2026-02-07 02:05:25 | 1 | ||||||||
|
Spike2 Software Resource Report Resource Website 100+ mentions |
Spike2 Software (RRID:SCR_000903) | software resource | THIS RESOURCE IS NO LONGER IN SERVICE.Documented on September 23,2022. A data acquisition and analysis software package for electrophysiology data. Spike2 software offers multi-channel continuous data acquisition and analysis with a multitude of options. This offers flexible usage from a simple chart recorder to complex applications requiring stimulus generation, data capture, scrolling or triggered displays, control of external equipment, and custom analysis. Spike2 software can be used in many fields such as electrophysiology, neurophysiology, cardiovascular and respiratory studies, sports science and pharmacology. | electrophysiology, eeg, neurophysiology, cardiovascular, respiratory, sports science, pharmacology, data acquisition, stimulus generation, data capture, continuous | works with: CED Power1401 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_156886, rid_000090 | SCR_000903 | Spike 2 software Cambridge Electronic Device, Spike2 | 2026-02-07 02:05:26 | 216 | ||||||||
|
NIH Office of Research on Women's Health; Bethesda; Maryland Resource Report Resource Website 1+ mentions |
NIH Office of Research on Women's Health; Bethesda; Maryland (RRID:SCR_000986) | ORWH, NIH ORWH | funding resource | The Office of Research on Women's Health (ORWH) is part of the Office of the Director of NIH. ORWH works in partnership with the 27 NIH Institutes and Centers to ensure that women’s health research is part of the scientific framework at the NIH and throughout the scientific community. | funding resource, office of research, women, health, nih women, orwh, women health research |
has parent organization: NIH Office of the Director has plug in: National Finals Rodeo 2018 live stream |
nlx_152796 | http://orwh.od.nih.gov/research/fundingopportunities.asp | SCR_000986 | NIH Office of Research on Womens Health, NIH Office of Research on Women's Health | 2026-02-07 02:05:29 | 4 | |||||||
|
National Taiwan University; Taipei; Taiwan Resource Report Resource Website 1+ mentions |
National Taiwan University; Taipei; Taiwan (RRID:SCR_000983) | NTU | university | A national research university in Taipei, Taiwan. The university confers degrees at the undergraduate and graduate level bio-resources and agriculture, electrical engineering and computer science, engineering, law, liberal arts, management, medicine, public health, and the social sciences. | national, research, law, finance, engineering, electrical, medicine, undergraduate, graduate |
is parent organization of: Library for Support Vector Machines is parent organization of: VNTR Locus Database is parent organization of: LIBSVM is parent organization of: TCMGeneDIT is parent organization of: Functional MRI Analysis and Clustering Tools is parent organization of: Oncogenomic Database of Hepatocellular Carcinoma is parent organization of: POINT: Prediction Of INTeractome |
Wikidata:Q32746, nlx_65230, ISNI:0000 0004 0546 0241, grid.19188.39, Crossref funder ID:501100006477 | https://ror.org/05bqach95 | SCR_000983 | 2026-02-07 02:05:29 | 1 | ||||||||
|
National University of Singapore; Singapore; Singapore Resource Report Resource Website 1+ mentions |
National University of Singapore; Singapore; Singapore (RRID:SCR_000984) | NUS | university | A public university located in Singapore that has a wide range of faculties and schools, including arts, business, computing, and dentistry. | public, singapore, art, business, computing, dentistry, design, architecture |
is parent organization of: imcalc: SPM batch image calculator is parent organization of: pfSNP is parent organization of: vis: SPM Visualized Statistics toolbox is parent organization of: AllerHunter: Cross-reactive Allergen Prediction Home is parent organization of: GBSA is parent organization of: Yong Loo Lin School of Medicine; Singapore; Singapore is parent organization of: Christopher Hogues Research Lab at the National University of Singapore is parent organization of: MBInfo is parent organization of: Therapeutic Target Database is parent organization of: DART - Drug Adverse Reaction Targets is parent organization of: Kinetic Data of Bio-molecular Interaction is parent organization of: MHC-Peptide Interaction Database is parent organization of: Xpro is parent organization of: Computed Ligand Binding Energy is parent organization of: Drosophila melanogaster Exon Database is parent organization of: Drug ADME Associated Protein Database is parent organization of: Trauma Screening Questionaire is parent organization of: Mixed Effect Model of Genetic-Set and Environment Interaction |
nlx_67014 | SCR_000984 | National University of Singapore | 2026-02-07 02:05:25 | 2 | ||||||||
|
CryptoBase Resource Report Resource Website 1+ mentions |
CryptoBase (RRID:SCR_000780) | software resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented July 19, 2016. This site is built and maintained by the Madhani Lab, Dept. of Biochemistry and Biophysics at the University of California, San Francisco | has parent organization: University of California at San Francisco; California; USA | Herb and Marion Sandler Foundation | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-30395 | http://archive.is/YgVX4 | SCR_000780 | 2026-02-07 02:05:25 | 2 | ||||||||
|
FileMaker Resource Report Resource Website 50+ mentions |
FileMaker (RRID:SCR_000783) | software resource | A database software for managing, analyzing and sharing information across multiple devices and people, both online and offline. | file, maker, information, sharing, analyze, sync, devices, windows, apple, ios, FASEB list | Restricted | nif-0000-30436 | SCR_000783 | FileMaker | 2026-02-07 02:05:25 | 65 | |||||||||
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GlycoWorkbench Resource Report Resource Website 1+ mentions |
GlycoWorkbench (RRID:SCR_000782) | software resource | A suite of software tools designed for the rapid drawing of glycan structures and for assisting the process of structure determination from mass spectrometry data. | rapid drawing of glycan structures |
is listed by: OMICtools has parent organization: Google Code |
PMID:23109548 | Free, Available for download, Freely available | OMICS_05691 | SCR_000782 | 2026-02-07 02:05:23 | 5 |
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