Searching the RRID Resource Information Network
Are you sure you want to leave this community? Leaving the community will revoke any permissions you have been granted in this community.
SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
IGB Resource Report Resource Website 100+ mentions |
IGB (RRID:SCR_011792) | IGB | software resource | An easy-to-use, highly customizable genome browser you can use to visualize and explore genomic data and annotations, including RNA-Seq, ChIP-Seq, tiling array data, and more. | genome, rna-seq, chip-seq, tiling array, browser |
is listed by: OMICtools has parent organization: University of North Carolina at Charlotte; North Carolina; USA |
PMID:19654113 | Free, Acknowledgement requested | OMICS_00916 | SCR_011792 | Integrated Genome Browser | 2026-09-19 12:52:18 | 354 | ||||||
|
Integrative Genomics Viewer Resource Report Resource Website 500+ mentions |
Integrative Genomics Viewer (RRID:SCR_011793) | IGV | software resource | A high-performance visualization tool for interactive exploration of large, integrated genomic datasets. | genomic datasets exploration, |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite has parent organization: Broad Institute |
DOI:10.1038/nbt.1754 | OMICS_00917, biotools:igv | https://bio.tools/igv, https://sources.debian.org/src/igv/ | SCR_011793 | 2026-09-19 12:52:18 | 878 | |||||||
|
NCBI Genome Workbench Resource Report Resource Website 10+ mentions |
NCBI Genome Workbench (RRID:SCR_011794) | Genome Workbench | software resource | An integrated application for viewing and analyzing sequence data. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: NCBI |
OMICS_00920, biotools:ncbi_genome_workbench | https://bio.tools/ncbi_genome_workbench | SCR_011794 | 2026-09-19 12:52:18 | 11 | ||||||||
|
ngs.plot Resource Report Resource Website 10+ mentions |
ngs.plot (RRID:SCR_011795) | ngs.plot | software resource | A software program that allows you to easily visualize your next-generation sequencing (NGS) samples at functional genomic regions. | bio.tools, FASEB list |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Google Code |
GNU General Public License, v3 | BioTools:ngs.plot, OMICS_00922, biotools:ngs.plot | https://bio.tools/ngs.plot, https://bio.tools/ngs.plot, https://bio.tools/ngs.plot | SCR_011795 | ngsplot, ngsplot - Quick mining and visualization of next-generation sequencing data by integrating genomic databases | 2026-09-19 12:52:18 | 45 | ||||||
|
MizBee Resource Report Resource Website 1+ mentions |
MizBee (RRID:SCR_011804) | MizBee | software resource | A multiscale synteny browser for exploring conservation relationships in comparative genomics data. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Utah; Utah; USA |
OMICS_00943, biotools:mizbee | https://bio.tools/mizbee | SCR_011804 | MizBee - A Multiscale Synteny Browser | 2026-09-19 12:52:18 | 2 | |||||||
|
PipMaker and MultiPipMaker Resource Report Resource Website 50+ mentions |
PipMaker and MultiPipMaker (RRID:SCR_011806) | PipMaker and MultiPipMaker | software resource | PipMaker computes alignments of similar regions in two DNA sequences. Moreover, MultiPipMaker can be requested to compute a true multiple alignment of the input sequences and return a nucleotide-level view of the results. |
is listed by: OMICtools has parent organization: Pennsylvania State University |
OMICS_00944 | SCR_011806 | 2026-09-19 12:52:18 | 78 | ||||||||||
|
SynBrowse Resource Report Resource Website 1+ mentions |
SynBrowse (RRID:SCR_011807) | SynBrowse | software resource | A generic sequence comparison tool for visualizing genome alignments both within and between species. | is listed by: OMICtools | OMICS_00946 | SCR_011807 | Synteny Browser | 2026-09-19 12:52:18 | 2 | |||||||||
|
ECHO Resource Report Resource Website 100+ mentions |
ECHO (RRID:SCR_011851) | ECHO | algorithm resource, data analysis software, data processing software, sequence analysis software, software application, software resource | Error correction algorithm designed for short-reads from next-generation sequencing platforms such as Illumina''s Genome Analyzer II. | error correction, rnaseq, rna sequence, short-read, next-generation sequencing, ngs, illumina, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:21482625 DOI:10.1101/gr.111351.110 |
Free, Available for download | biotools:echo, OMICS_01102 | https://bio.tools/echo, https://sources.debian.org/src/uc-echo/ | SCR_011851 | ECHO: A reference-free short-read error correction algorithm | 2026-09-19 12:52:19 | 312 | |||||
|
CANGS Resource Report Resource Website 1+ mentions |
CANGS (RRID:SCR_011837) | CANGS | data analysis software, data processing software, software application, software resource | A user-friendly utility for processing and analyzing 454 GS-FLX data in biodiversity studies. | windows, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite |
PMID:20180949 | biotools:cangs, OMICS_01084 | https://bio.tools/cangs | SCR_011837 | 2026-09-19 12:52:19 | 1 | |||||||
|
ConDeTri Resource Report Resource Website 50+ mentions |
ConDeTri (RRID:SCR_011838) | ConDeTri | software resource | Software tool as content dependent read trimmer for Illumina data. Content dependent read trimming software for Illumina/Solexa sequencing data. | Solexa sequencing data, Illumina data, data read trimming, read trimmer, sequencing data, |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:22039460 | Free, Available for download, Freely available | OMICS_01085, biotools:condetri | https://bio.tools/condetri, https://sources.debian.org/src/condetri/, https://github.com/linneas/condetri/ | SCR_011838 | 2026-09-19 12:52:19 | 67 | ||||||
|
Quake Resource Report Resource Website 50+ mentions |
Quake (RRID:SCR_011839) | Quake | software resource | A software package to correct substitution sequencing errors in experiments with deep coverage (e.g. >15X), specifically intended for Illumina sequencing reads. |
is listed by: OMICtools has parent organization: University of Maryland; Maryland; USA |
OMICS_01106 | SCR_011839 | 2026-09-19 12:52:19 | 80 | ||||||||||
|
SBEAMS Resource Report Resource Website 1+ mentions |
SBEAMS (RRID:SCR_011830) | SBEAMS | software resource | Software providing a framework for collecting, storing, and accessing data produced by a wide variety of experiments. | proteomics, microarray | is listed by: OMICtools | PMID:16756676 | OMICS_01011 | SCR_011830 | Systems Biology Experiment Analysis Management System | 2026-09-19 12:52:19 | 9 | |||||||
|
Circos Resource Report Resource Website 5000+ mentions |
Circos (RRID:SCR_011798) | Circos | software resource | A software package for visualizing data and information. It visualizes data in a circular layout - this makes Circos ideal for exploring relationships between objects or positions. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: JupiterPlot |
DOI:10.1101/gr.092759.109 | biotools:circos, OMICS_00932 | https://bio.tools/circos, https://sources.debian.org/src/circos/ | SCR_011798 | 2026-09-19 12:52:18 | 5669 | |||||||
|
G-compass Resource Report Resource Website 1+ mentions |
G-compass (RRID:SCR_011799) | G-compass | software resource | It visualizes evolutionarily conserved genomic regions between human and other 12 vertebrates based on original genome alignments pursuing higher coverage. | is listed by: OMICtools | OMICS_00934 | SCR_011799 | 2026-09-19 12:52:18 | 1 | ||||||||||
|
discovering-cse Resource Report Resource Website |
discovering-cse (RRID:SCR_011832) | discovering-cse | software resource | Software for discovering motifs that induce sequencing errors. | motif |
is listed by: OMICtools has parent organization: Google Code |
GNU General Public License, v3 | OMICS_01040 | SCR_011832 | Discovering Context-Specific Sequencing Errors | 2026-09-19 12:52:19 | 0 | |||||||
|
MT-Toolbox Resource Report Resource Website 1+ mentions |
MT-Toolbox (RRID:SCR_011833) | MT-Toolbox | software resource | A software package for building accurate ConSeqs from tagged reads. | is listed by: OMICtools | PMID:23995388 | BSD License | OMICS_01058 | SCR_011833 | Molecule Tag Toolbox | 2026-09-19 12:52:19 | 4 | |||||||
|
AlienTrimmer Resource Report Resource Website 50+ mentions |
AlienTrimmer (RRID:SCR_011835) | AlienTrimmer | software resource | Allows detecting and removing multiple alien sequences in both ends of sequence reads. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:23912058 | Free | biotools:alientrimmer, OMICS_01082 | https://bio.tools/alientrimmer | SCR_011835 | 2026-09-19 12:52:19 | 74 | ||||||
|
QTrim Resource Report Resource Website 1+ mentions |
QTrim (RRID:SCR_011842) | QTrim | software resource | A next generation sequence quality trimming tool. | is listed by: OMICtools | OMICS_01089 | SCR_011842 | 2026-09-19 12:52:19 | 6 | ||||||||||
|
sabre Resource Report Resource Website 100+ mentions |
sabre (RRID:SCR_011843) | sabre | data analysis software, data processing software, software application, software resource | Software tool to demultiplex barcoded reads into separate files. Works on both single-end and paired-end data in fastq format. Used in next generation sequencing to analyze a broad range of data. | demultiplex, bardcode, separate, fastq, format, data, next, generation, sequencing, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
Free, Available for download, Freely available | biotools:sabre, OMICS_01090 | https://bio.tools/sabre | SCR_011843 | Systems Approach to Biomarker Research | 2026-09-19 12:52:19 | 219 | ||||||
|
Scythe Resource Report Resource Website 100+ mentions |
Scythe (RRID:SCR_011844) | Scythe | software resource | Scythe uses a Naive Bayesian approach to classify contaminant substrings in sequence reads. |
is listed by: OMICtools is listed by: Debian |
OMICS_01091 | https://sources.debian.org/src/scythe/ | SCR_011844 | Scythe - A Bayesian adapter trimmer | 2026-09-19 12:52:19 | 189 |
Can't find your Tool?
We recommend that you click next to the search bar to check some helpful tips on searches and refine your search firstly. Alternatively, please register your tool with the SciCrunch Registry by adding a little information to a web form, logging in will enable users to create a provisional RRID, but it not required to submit.
Welcome to the RRID Resources search. From here you can search through a compilation of resources used by RRID and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that RRID has compiled. You can navigate through those categories from here or change to a different tab to execute your search through. Each tab gives a different perspective on data.
If you have an account on RRID then you can log in from here to get additional features in RRID such as Collections, Saved Searches, and managing Resources.
Here is the search term that is being executed, you can type in anything you want to search for. Some tips to help searching:
If you are logged into RRID you can add data records to your collections to create custom spreadsheets across multiple sources of data.
Here are the facets that you can filter the data by.
If you have any further questions please check out our FAQs Page to ask questions and see our tutorials. Click this button to view this tutorial again.
