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.
https://hci-bio-app.hci.utah.edu/gnomex/
A Genomic Laboratory Information Management System (LIMS) and Data repository that can function as an experiment tracking and workflow management system for Core Facilities as well as an advanced data repository for storing and sharing genomic data sets.
Proper citation: GNomEx (RRID:SCR_011805) Copy
Software for searching DNA sequence databases for RNA structure and sequence similarities.
Proper citation: Infernal (RRID:SCR_011809) Copy
http://www.ige.tohoku.ac.jp/joho/gmProject/gmhome.html
A graphical interface for comparative genomics.
Proper citation: GenomeMatcher (RRID:SCR_011800) Copy
http://www-ps.informatik.uni-tuebingen.de/itNew/?page_id=1160
Alignment visualization based on SuperGenome coordinates.
Proper citation: GenomeRing (RRID:SCR_011801) Copy
An interactive, web-based tool for comparative genomic visualization.
Proper citation: Gobe (RRID:SCR_011802) Copy
http://cas-bioinfo.cas.unt.edu/gsv/homepage.php
Software that allows users to upload files which contain synteny regions between two or more genomes and interactively visualize the synteny between them.
Proper citation: GSV (RRID:SCR_011803) Copy
https://www.softgenetics.com/NextGENe.php
Software tool for Next Generation sequence analysis. Analytical partner for analysis of desktop sequencing data produced by Illumina iSeq, Miniseq, MiSeq, NextSeq, HiSeq, and NovaSeq systems, Ion Torrent Ion GeneStudio S5, PGM, and Proton systems as well as other platforms. Software runs on Windows Operating System, which provides biologist friendly interface. It does not require scripting or other bioinformatics support.
Proper citation: NextGENe (RRID:SCR_011859) Copy
http://www.csd.uwo.ca/~ilie/RACER/
A software program for correcting errors in sequencing data.
Proper citation: RACER (RRID:SCR_011852) Copy
Automates the primary analysis of massive parallel sequencing data.
Proper citation: NARWHAL (RRID:SCR_011858) Copy
http://utgenome.org/index.html
An open-source software for developing personalized genome browsers that work in web browsers.
Proper citation: UTGB Toolkit (RRID:SCR_011797) Copy
https://github.com/MikkelSchubert/adapterremoval
Software program to remove residual adapter sequences from next generation sequencing reads. Used for cleaning of next-generation sequencing reads. AdapterRemoval v2 introduces improvements in throughput, through use of single instruction, multiple data (SIMD; SSE1 and SSE2) instructions and multi-threading support; handles datasets containing reads or read-pairs with different adapters or adapter pairs; provides simultaneous demultiplexing and adapter trimming; has ability to reconstruct adapter sequences from paired-end reads for poorly documented data sets; provides native gzip and bzip2 support.
Proper citation: AdapterRemoval (RRID:SCR_011834) Copy
http://graphics.med.yale.edu/trim/
A fast and lightweight software to trim adapters and low quality regions in reads from ultra high-throughput next-generation sequencing machines.
Proper citation: Btrim (RRID:SCR_011836) Copy
http://www.cs.helsinki.fi/u/lmsalmel/coral/
An error correction algorithm for correcting reads from DNA sequencing platforms such as the Illumina Genome Analyzer or HiSeq platforms or Roche/454 Genome Sequencer.
Proper citation: Coral (RRID:SCR_011849) Copy
http://www.genome.umd.edu/quorum.html
Software tool as error corrector for Illumina reads. It is distributed and used with MaSuRCA, or it can be used independently.
Proper citation: QuorUM (RRID:SCR_011840) Copy
http://code.google.com/p/cutadapt/
Software tool that removes adapter sequences from DNA sequencing reads., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: cutadapt (RRID:SCR_011841) Copy
Graphical user interface software for metadata-driven management, analysis, and visualization of microbiome data.
Proper citation: Explicet (RRID:SCR_011937) Copy
An online toolbox for metagenomic data visualization.
Proper citation: MetaSee (RRID:SCR_011938) Copy
http://genopole.pasteur.fr/SynTView/
An interactive multi-view genome browser for next-generation comparative microorganism genomics.
Proper citation: SynTView (RRID:SCR_011939) Copy
http://ccb.jhu.edu/software/glimmer/index.shtml
A software system for finding genes in microbial DNA, especially the genomes of bacteria, archaea, and viruses.
Proper citation: Glimmer (RRID:SCR_011931) Copy
http://cbb.sjtu.edu.cn/~ccwei/pub/software/NeSSM.php
A Next-Generation Sequencing Simulator for Metagenomics.
Proper citation: NeSSM (RRID:SCR_011941) Copy
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 dkNET Resources search. From here you can search through a compilation of resources used by dkNET and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that dkNET 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 dkNET then you can log in from here to get additional features in dkNET 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:
You can save any searches you perform for quick access to later from here.
We recognized your search term and included synonyms and inferred terms along side your term to help get the data you are looking for.
If you are logged into dkNET you can add data records to your collections to create custom spreadsheets across multiple sources of data.
Here are the sources that were queried against in your search that you can investigate further.
Here are the categories present within dkNET that you can filter your data on
Here are the subcategories present within this category that you can filter your data on
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.
The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
Email: info_at_ dknet.org
