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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://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
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
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
http://xmedcon.sourceforge.net/
Open source software toolkit for medical image conversion.
Proper citation: XMedCon (RRID:SCR_024366) Copy
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
https://github.com/miRTop/mirtop
Command lines tool to annotate miRNAs with standard mirna/isomir naming.
Proper citation: mirtop (RRID:SCR_024116) Copy
https://sourceforge.net/projects/mpsqed/
Software tool for the design of multiplex pyrosequencing assays.
Proper citation: mPSQed (RRID:SCR_024118) Copy
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
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
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
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
https://github.com/fhcrc/seqmagick/
Software application to expose file format conversion in BioPython in convenient way. Imagemagick like frontend to Biopython SeqIO.
Proper citation: seqmagick (RRID:SCR_024331) Copy
https://github.com/WorkflowConversion/CTDopts
Software gives your command-line tools a CTD-compatible interface. Module for enabling tools with CTD reading/writing, argument parsing, validating and manipulating capabilities.
Proper citation: CTDopts (RRID:SCR_023997) Copy
https://github.com/jkbonfield/htscodecs/
Software repository implements the custom CRAM codecs used for "EXTERNAL" block types.Custom compression for CRAM custom algorithm written to compress the BAM file format for DNA sequencing data.
Proper citation: Htscodecs (RRID:SCR_024034) Copy
https://github.com/conda/conda-package-handling
Software to create and extract conda packages of various formats.
Proper citation: conda-package-handling (RRID:SCR_023991) Copy
http://www.cbcb.umd.edu/software/ELPH/index.shtml
Software tool as general purpose Gibbs sampler for finding motifs in set of DNA or protein sequences.Takes as input a set containing sequences, and searches through them for the most common motif, assuming that each sequence contains one copy of the motif. Used to find patterns such as ribosome binding sites (RBSs) and exon splicing enhancers (ESEs).
Proper citation: ELPH (RRID:SCR_024011) Copy
https://github.com/PacificBiosciences/unanimity
Software to generate highly accurate single molecule consensus reads.
Proper citation: CCS (RRID:SCR_024379) Copy
https://github.com/cancerit/alleleCount
Software package to prevent code duplication. Support code for NGS copy number algorithms. Generates count of coverage of each allele ACGT at that location given any filter settings.
Proper citation: alleleCount (RRID:SCR_023961) Copy
https://github.com/mateidavid/fast5
Software C++ library for accessing Oxford Nanopore Technologies sequencing data.
Proper citation: Fast5 Library (RRID:SCR_024023) Copy
Software provides command line interface and Python API for working with Biological Observation Matrix files.
Proper citation: python-biom-format (RRID:SCR_024193) Copy
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