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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
miRNAKey Resource Report Resource Website 1+ mentions |
miRNAKey (RRID:SCR_004813) | miRNAKey | software resource | A software pipeline for the analysis of microRNA Deep Sequencing data. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:20801911 | OMICS_00364, biotools:mirnakey | https://bio.tools/mirnakey | SCR_004813 | 2026-08-01 12:02:45 | 6 | |||||||
|
SVMerge Resource Report Resource Website 10+ mentions |
SVMerge (RRID:SCR_004777) | SVMerge | software resource | Software pipeline to detect structural variants (SVs) by integrating calls from several existing SV callers, which are then validated and the breakpoints refined using local de novo assembly. The output is in BED format allowing for easy downstream analysis or viewing in a genome browser. It is modular and extensible allowing new callers to be incorporated as they become available. | structural variant, breakpoint, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
PMID:21194472 | biotools:svmerge, OMICS_00325 | https://bio.tools/svmerge | SCR_004777 | SVMerge - Enhanced structural variant and breakpoint detection | 2026-08-01 12:02:40 | 19 | ||||||
|
SVseq Resource Report Resource Website 1+ mentions |
SVseq (RRID:SCR_004804) | SVseq | software resource | Software for accurate and efficient calling of structural variations with low-coverage sequence data. Version 2 uses the BAM files of paired Illumina reads with soft-clip signature as input. It calls both deletions and insertions. | structural variant, deletion, insertion, breakpoint, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University of Connecticut; Connecticut; USA |
PMID:22537045 | OMICS_00327, biotools:svseq | https://bio.tools/svseq | SCR_004804 | SVseq2, SVseq1 | 2026-08-01 12:02:46 | 3 | ||||||
|
Minia Resource Report Resource Website 50+ mentions |
Minia (RRID:SCR_004986) | Minia | software resource | A short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
DOI:10.1186/1748-7188-8-22 | biotools:minia, OMICS_00022 | https://bio.tools/minia, https://sources.debian.org/src/minia/ | SCR_004986 | 2026-08-01 12:02:43 | 62 | |||||||
|
TemplateFilter Resource Report Resource Website 1+ mentions |
TemplateFilter (RRID:SCR_004980) | TemplateFilter | software resource | A software pipeline for analyzing deep sequencing maps of chromatin structure. |
is listed by: OMICtools has parent organization: Hebrew University of Jerusalem; Jerusalem; Israel |
Free for academic use, GNU General Public License | OMICS_00514 | SCR_004980 | 2026-08-01 12:02:43 | 1 | |||||||||
|
UPARSE Resource Report Resource Website 1000+ mentions |
UPARSE (RRID:SCR_005020) | UPARSE | software resource | An Operational Taxonomic Unit (OTU) clustering software for 16S and other marker genes. Highly accurate OTU sequences and improved diversity measures. | is listed by: OMICtools | PMID:23955772 | OMICS_01449 | SCR_005020 | 2026-08-01 12:02:44 | 3898 | |||||||||
|
CARMA Resource Report Resource Website 50+ mentions |
CARMA (RRID:SCR_004999) | CARMA | software resource | A software pipeline for characterizing the taxonomic composition and genetic diversity of short-read metagenomes. The software was originally designed for the analysis of environmental metagenomes obtained by the ultra-fast 454 pyrosequencing system. | metagenome, phylogenetic, dna fragment, dna, classification |
is listed by: OMICtools has parent organization: Bielefeld University; North Rhine-Westphalia; Germany |
PMID:18285365 | Acknowledgement requested | OMICS_01451 | SCR_004999 | CARMA - Characterizing Short Read Metagenomes | 2026-08-01 12:02:44 | 86 | ||||||
|
MiTCR Resource Report Resource Website 10+ mentions |
MiTCR (RRID:SCR_004989) | MiTCR | software resource | An open source software package aimed at extraction of information on repertoire of T-cell clones from Next Generation Sequencing (NGS) data. It is designed with the knowledge of the critical challenges arising in everyday processing of immunological data. | next generation sequencing | is listed by: OMICtools | PMID:23892897 | Apache License | OMICS_00003 | SCR_004989 | MiTCR - T-cell receptor repertoire analysis software | 2026-08-01 12:02:43 | 34 | ||||||
|
MIP Scaffolder Resource Report Resource Website 1+ mentions |
MIP Scaffolder (RRID:SCR_005072) | MIP Scaffolder | software resource | A software program for scaffolding contigs produced by fragment assemblers using mate pair data such as those generated by ABI SOLiD or Illumina Genome Analyzer. | scaffolding, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Helsinki; Helsinki; Finland |
OMICS_00044, biotools:mip_scaffolder | https://bio.tools/mip_scaffolder | SCR_005072 | 2026-08-01 12:02:53 | 1 | ||||||||
|
Scarpa Resource Report Resource Website 10+ mentions |
Scarpa (RRID:SCR_005073) | Scarpa | software resource | A stand-alone scaffolding tool for NGS data. It can be used together with virtually any genome assembler and any NGS read mapper that supports SAM format. Other features include support for multiple libraries and an option to estimate insert size distributions from data. | scaffolding |
is listed by: OMICtools has parent organization: University of Toronto; Ontario; Canada |
PMID:23274213 | GNU General Public License | OMICS_00047 | SCR_005073 | SCARPA: scaffolding reads with practical algorithms, Scaffolding Reads with Practical Algorithms | 2026-08-01 12:02:45 | 13 | ||||||
|
T-lex Resource Report Resource Website 1+ mentions |
T-lex (RRID:SCR_005134) | T-lex | software resource | Software package for fast and accurate discovery, annotation, re-annotation and population analysis of Transposable Elements using Next-Generation Sequencing data. | transposable element, next-generation sequencing, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Stanford University; Stanford; California has parent organization: SourceForge |
GNU General Public License | biotools:t-lex2, OMICS_00121 | https://bio.tools/t-lex2 | SCR_005134 | T-lex package | 2026-08-01 12:02:46 | 4 | ||||||
|
PoPoolation TE Resource Report Resource Website 1+ mentions |
PoPoolation TE (RRID:SCR_005131) | PoPoolation TE | software resource | A quick and simple pipeline for the analysis of transposable element (TE) insertions in (natural) populations using next generation sequencing. It calculates TE insertion frequencies for TEs that are present in the reference genome as well as for novel TE insertions. PoPoolation TE requires paired-end reads from a pooled population, a reference sequence and transposable element sequences (fasta-file). | next generation sequencing, transposable element, insertion frequency, genomics, population genetics, illumina |
is listed by: OMICtools has parent organization: Google Code |
PMID:22291611 | Acknowledgement requested, New BSD License | OMICS_00119 | SCR_005131 | 2026-08-01 12:02:46 | 1 | |||||||
|
BEERS Resource Report Resource Website 10+ mentions |
BEERS (RRID:SCR_005090) | BEERS | software resource | A simulation engine for generating RNA-Seq data that was designed to benchmark RNA-Seq alignment algorithms and also algorithms that aim to reconstruct different isoforms and alternate splicing from RNA-Seq data. By default BEERS simulates either mouse or human paired-end RNA-Seq data modeled on the illumina platform. It starts with a large number of gene models (approx 500K) taken from about ten different published annotation efforts, and then chooses a fixed number of these genes at random (30,000 by default). This avoids biasing for or against any particular set of annotations. BEERS then introduces substitutions, indels, alternate spice forms, sequencing errors, and intron signal. BEERS can also simulate strand specific reads. BEERS does not simulate quality scores. There are four configuration files required, these are available for human and mouse. BEERS can also be configured to use any set of gene models. Pre-built indexes for human refseq are given. Using these indexes will generate a much tamer set of transcripts. BEERS is written in perl. | perl, rna-seq |
is listed by: OMICtools has parent organization: University of Pennsylvania Perelman School of Medicine; Pennsylvania; USA |
PMID:21775302 | OMICS_01364 | SCR_005090 | Benchmarker for Evaluating the Effectiveness of RNA-Seq Software (BEERS), Benchmarker for Evaluating the Effectiveness of RNA-Seq Software | 2026-08-01 12:02:54 | 22 | |||||||
|
ERANGE Resource Report Resource Website 10+ mentions |
ERANGE (RRID:SCR_005240) | ERANGE | software resource | Software for Mapping and Quantifying Mammalian Transcriptomes by RNA-Seq. Its functions are to (i) assign reads that map uniquely in the genome to their site of origin and, for reads that match equally well to several sites (''multireads''), assign them to their most likely site(s) of origin; (ii) detect splice-crossing reads and assign them to their gene of origin; (iii) organize reads that cluster together, but do not map to an already known exon, into candidate exons or parts of exons; and (iv) calculate the prevalence of transcripts from each known or newly proposed RNA, based on normalized counts of unique reads, spliced reads and multireads. The new candidate RNA regions produced can be thought of as ESTs, and, like ESTs, some are provisionally appended to existing gene models if they meet several additional criteria. Remaining unassigned candidate transcribed regions (labeled RNAFAR features) can then be used in conjunction with other confirming data to develop new or revised gene models. | transcriptome, rna-seq, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:18516045 | OMICS_01274, biotools:erange | https://bio.tools/erange | SCR_005240 | Enhanced Read Analysis of Gene Expression | 2026-08-01 12:02:58 | 30 | ||||||
|
RNA-SeQC Resource Report Resource Website 100+ mentions |
RNA-SeQC (RRID:SCR_005120) | RNA-SeQC | software resource | Java software which computes a series of quality control metrics for RNA-seq data and can compare sequencing quality across different samples or experiments to evaluate different experimental parameters. The input can be one or more BAM files, and the output consists of HTML reports and tab delimited files of metrics data. | java, bam file, html, sequence comparison, rnaseq, rna sequence, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Broad Institute |
PMID:22539670 | Acknowledgement requested, Public | biotools:rna-seqc, OMICS_01234 | https://bio.tools/rna-seqc | SCR_005120 | 2026-08-01 12:02:49 | 203 | ||||||
|
Flux Simulator Resource Report Resource Website 1+ mentions |
Flux Simulator (RRID:SCR_005088) | Flux Simulator | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 5, 2023. Software that aims at modeling RNA-Seq experiments in silico: sequencing reads are produced from a reference genome according annotated transcripts. The simulation pipeline models different steps as modules, each with a minimal set of parameters that can be estimated by experimental parameters. The first step is-in fact-a transcriptome simulator. Subsequently, common sources of systematic bias in the abundance and distribution of produced reads are simulated by in silico library preparation and sequencing. | is listed by: OMICtools | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01365 | SCR_005088 | 2026-08-01 12:02:45 | 2 | |||||||||
|
jobs.ac.uk Resource Report Resource Website 1+ mentions |
jobs.ac.uk (RRID:SCR_005154) | jobs.ac.uk | job resource | International job board for careers in academic, research, science and related professions in the UK, Europe, Australasia, Africa, America and Asia & Middle East. Launched by the University of Warwick, they have grown to become the top recruitment site in their sector, attracting the most qualified and talented people from the UK, Europe and across the world. Users may subscribe to Jobs by Email for vacancies in universities, colleges, research institutions, commercial and public sector, schools and charities. You may upload your CV to give yourself an advantage by making your CV visible to top employers now! | job seeker, employer, career, curriculum vitae, recruit, employment, database, data storage repository |
is used by: NIF Data Federation is listed by: OMICtools is related to: Integrated Jobs has parent organization: University of Warwick; Coventry; United Kingdom |
The community can contribute to this resource | OMICS_01829, nlx_144167 | SCR_005154 | 2026-08-01 12:02:47 | 2 | ||||||||
|
methylKit Resource Report Resource Website 500+ mentions |
methylKit (RRID:SCR_005177) | methylKit | software resource | An R package for DNA methylation analysis and annotation from high-throughput bisulfite sequencing., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. |
is listed by: OMICtools has parent organization: Google Code |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00606 | SCR_005177 | 2026-08-01 12:02:57 | 617 | |||||||||
|
GESND Resource Report Resource Website |
GESND (RRID:SCR_005179) | GESND | software resource | A software package and a pipeline for identifying causal mutations for rare congenital diseases by next-generation sequencing. Features * one-stop solution for identifying causal mutations of rare genetic diseases * detect wide-spctrum variants, including medium and large sized indels, and tandem repeats * annotate and filter variants * prioritize candidate variants | next-generation sequencing, mutation, variant, indel, tandem repeat |
is listed by: OMICtools has parent organization: SourceForge |
Rare congenital disease | OMICS_00175 | SCR_005179 | Genetic Screening and Diagnosis, GESND - Genetic Screening and Diagnosis | 2026-08-01 12:02:47 | 0 | |||||||
|
CHAoS Resource Report Resource Website 10+ mentions |
CHAoS (RRID:SCR_005174) | CHAoS | software resource | A Perl-based system for annotation of variants identified in high-throughput sequencing experiments. Functionality includes annotation of variants with information relating to population genetics, known transcripts, positional records, and sequence motif-based prediction. In addition, annotated variants can be summarized and extracted to facilitate downstream analysis. There is also basic support for gene-based biological annotation, and eventually will include tools for variant and genotype analysis and visualization. | annotation, analysis, visualization, variant, high-throughput sequencing, perl, population genetic, transcript, positional record, sequence, motif, genotype |
is listed by: OMICtools has parent organization: Wellcome Trust Centre for Human Genetics |
GNU General Public License, v2 | OMICS_00170 | SCR_005174 | chaos - Annotation analysis and visualization of variants from high-throughput sequencing experiments | 2026-08-01 12:02:47 | 26 |
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