Tools   Select Another Resource Report Type

https://github.com/tseemann/VelvetOptimiser/

Software tool to run as wrapper script for Velvet assembler and to assist with optimising the assembly.Used to search supplied hash value range for optimum, estimates expected coverage and then searches for optimum coverage cutoff. Estimates insert lengths for paired end libraries. Can optimise assemblies by default optimisation condition or by user supplied one. It outputs the results to subdirectory and records all its operations in logfile.

Proper citation: VelvetOptimiser (RRID:SCR_024376) Copy   

•   Source: SciCrunch Registry

http://visit.llnl.gov/

Open source software interactive, scalable, visualization, animation and analysis tool. Used to generate visualizations, animate them through time, manipulate them with variety of operators and mathematical expressions, and save resulting images and animations for presentations.

Proper citation: VisIt (RRID:SCR_024370) Copy   

•   Source: SciCrunch Registry

https://desmid.github.io/mview/

Web-compatible database search or multiple alignment viewer, Software tool as command line utility that extracts and reformats the results of a sequence database search or a multiple alignment, optionally adding HTML markup for web page layout. It can also be used as a filter to extract and convert searches or alignments to common formats.

Proper citation: MView (RRID:SCR_024129) Copy   

•   Source: SciCrunch Registry

http://rambok.sourceforge.net/

Software tool for rapid and sensitive removal of background sequences from Next Generation Sequencing data.

Proper citation: rambo-k (RRID:SCR_024198) Copy   

•   Source: SciCrunch Registry

https://web.archive.org/web/20180316202959/http://zombie.cb.k.u-tokyo.ac.jp/sprai/

Software tool to correct sequencing errors in single pass reads for de novo assembly.

Proper citation: sprai (RRID:SCR_024353) Copy   

•   Source: SciCrunch Registry

https://github.com/streamlit/streamlit

Software tool to turn data scripts into shareable web apps in minutes. Faster way to build and share data apps.

Proper citation: streamlit (RRID:SCR_024354) Copy   

•   Source: SciCrunch Registry

https://cme.h-its.org/exelixis/web/software/sweed/

Software tool for likelihood based detection of selective sweeps in thousands of genomes. Software parallel and checkpointable tool that implements composite likelihood ratio test for detecting selective sweeps.

Proper citation: sweed (RRID:SCR_024357) Copy   

•   Source: SciCrunch Registry

https://metacpan.org/dist/Bio-Tools-Run-Alignment-TCoffee

Software object for calculation of multiple sequence alignment from set of unaligned sequences or alignments using the TCoffee program.

Proper citation: Bio-Tools-Run-Alignment-TCoffee (RRID:SCR_024070) Copy   

•   Source: SciCrunch Registry

https://github.com/magnusmanske/snpomatic

Short read mapping software. Read mapping tool offering variety of analytical output functions, with emphasis on genotyping,

Proper citation: snpomatic (RRID:SCR_024348) Copy   

•   Source: SciCrunch Registry

http://www.workrave.org/

Software tool to assist in recovery and prevention of Repetitive Strain Injury. Monitors keyboard and mouse usage and using this information, it frequently alerts you to take microbreaks, rest breaks and restricts you to your daily computer usage.

Proper citation: Workrave (RRID:SCR_024364) Copy   

•   Source: SciCrunch Registry

http://xmedcon.sourceforge.net/

Open source software toolkit for medical image conversion.

Proper citation: XMedCon (RRID:SCR_024366) Copy   

•   Source: SciCrunch Registry

http://www.ks.uiuc.edu/Research/vmd/

Software tool as molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. VMD supports computers running MacOS X, Unix, or Windows, is distributed free of charge, and includes source code.

Proper citation: VMD (RRID:SCR_024368) Copy   

•   Source: SciCrunch Registry

https://github.com/miRTop/mirtop

Command lines tool to annotate miRNAs with standard mirna/isomir naming.

Proper citation: mirtop (RRID:SCR_024116) Copy   

•   Source: SciCrunch Registry

https://sourceforge.net/projects/mpsqed/

Software tool for the design of multiplex pyrosequencing assays.

Proper citation: mPSQed (RRID:SCR_024118) Copy   

•   Source: SciCrunch Registry

http://www-igm.univ-mlv.fr/~marsan/smile_english.html

Software tool that infers motifs in set of sequences to infer exceptionnal sites as binding sites in DNA sequences. 1.4 version allows to infer motifs written on any alphabet in any kind of sequences. Allows to deal with motifs associated by some distance constraints. Used to group under unique model different occurrences composed of several boxes separated by spacers of different lengths.

Proper citation: SMILE (RRID:SCR_024119) Copy   

•   Source: SciCrunch Registry

http://technelysium.com.au/?page_id=13

Software ideal for the most basic of sequencing projects, where assembly of multiple sequences is not required., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Chromas (RRID:SCR_000598) Copy   

•   Source: SciCrunch Registry

http://decgpu.sourceforge.net/homepage.htm

Software tool as parallel and distributed error correction algorithm for high-throughput short reads using CUDA and MPI parallel programming models.

Proper citation: DecGPU (RRID:SCR_000585) Copy   

•   Source: SciCrunch Registry

http://www.bioinf.uni-leipzig.de/Software/RNAplex/

Software tool to rapidly search for short interactions between two long RNAs.

Proper citation: RNAplex (RRID:SCR_002763) Copy   

•   Source: SciCrunch Registry

https://docs.igdiscover.se/en/stable/

Software to analyze antibody repertoires and discover new V genes from high-throughput sequencing reads.Heavy chains, kappa and lambda light chains are supported (to discover VH, VK and VL genes)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: IgDiscover (RRID:SCR_024037) Copy   

•   Source: SciCrunch Registry

https://www.sanger.ac.uk/science/tools/caf

Software tools for manipulating Common Assembly Format files text format for describing sequence assemblies,that can be downloaded from the Sanger ftp site.

Proper citation: caftools (RRID:SCR_023982) Copy   

•   Source: SciCrunch Registry