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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.
| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Bio-Graphics Resource Report Resource Website |
Bio-Graphics (RRID:SCR_024061) | software resource, software toolkit | Software package to generate GD images of Bio::Seq objects. | generate GD images of Bio::Seq objects, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/libbio-graphics-perl/ | SCR_024061 | Bio-Graphics - Generate GD images of Bio-Seq objects, libbio-graphics-perl | 2026-09-19 12:56:17 | 0 | ||||||||
|
pbcopper Resource Report Resource Website |
pbcopper (RRID:SCR_024152) | software library, software resource, software toolkit | Software library provides suite of data structures, algorithms, and utilities for PacBio C++ applications. | data structures, algorithms, utilities for PacBio C++ applications, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/pbcopper/ | SCR_024152 | 2026-09-19 12:56:19 | 0 | |||||||||
|
CLI for BioMAJ Resource Report Resource Website |
CLI for BioMAJ (RRID:SCR_023980) | software resource, software toolkit | Software package to use BioMAJ providing biomaj-cli. | is listed by: Debian | Free, Available for download, Freely available | https://sources.debian.org/src/biomaj3-cli/ | SCR_023980 | biomaj3-cli, biomaj-cli | 2026-09-19 12:56:17 | 0 | |||||||||
|
BCALM 2 Resource Report Resource Website 1+ mentions |
BCALM 2 (RRID:SCR_023975) | software application, software resource, source code | Software tool for constructing compacted de Bruijn graph from sequencing data.Parallel algorithm that distributes the input based on minimizer hashing technique, allowing for good balance of memory usage throughout its execution. | constructing compacted de Bruijn graph, sequencing data, | is listed by: Debian | PMID:27307618 | Free, Available for download, Freely available | OMICS_12164 | https://sources.debian.org/src/bcalm/ | SCR_023975 | bcalm | 2026-09-19 12:56:17 | 3 | ||||||
|
GCLib Resource Report Resource Website |
GCLib (RRID:SCR_024028) | software library, software resource, software toolkit | Software genomic C++ library of reusable code for bioinformatics projects.Provides core collection of data structures, trying to avoid unnecessary code dependencies of other heavy libraries, while minimizing build time. | reusable code for bioinformatics, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/gclib/ | SCR_024028 | gclib, genome-code-lib | 2026-09-19 12:56:17 | 0 | ||||||||
|
CAT and BAT Resource Report Resource Website 1+ mentions |
CAT and BAT (RRID:SCR_023988) | software resource, software toolkit | Software pipeline for taxonomic classification of contigs and metagenome-assembled genomes. Contig Annotation Tool and Bin Annotation Tool for the taxonomic classification of long DNA sequences and metagenome assembled genomes of both known and unknown microorganisms, as generated by contemporary metagenomics studies. | taxonomic classification, long DNA sequences, metagenome assembled genomes, known and unknown microorganisms, contemporary metagenomics studies, | is listed by: Debian | PMID:31640809 | Free, Available for download, Freely available | https://sources.debian.org/src/cat-bat/ | SCR_023988 | Bin Annotation Tool, Contig Annotation Tool, BAT, CAT, cat-bat, CAT/BAT | 2026-09-19 12:56:17 | 3 | |||||||
|
limereg Resource Report Resource Website |
limereg (RRID:SCR_024097) | software library, software resource, software toolkit | Open source commandline based application and/or software development library, that performs 2D, rigid image registration on two greyscale images and outputs either the transformation parameters or the registered image. | 2D, rigid image registration, greyscale images, transformation parameters, registered image, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/limereg/ | SCR_024097 | 2026-09-19 12:56:18 | 0 | |||||||||
|
NeoBio Resource Report Resource Website |
NeoBio (RRID:SCR_024131) | software library, software resource, software toolkit | Software library of sequence alignment algorithms implemented in Java. | bioinformatics algorithms implemented in Java, sequence alignment algorithms, | is listed by: Debian | Free, Available for download, Freely available, | OMICS_21450 | https://sources.debian.org/src/neobio/ | SCR_024131 | neobio | 2026-09-19 12:56:18 | 0 | |||||||
|
Murasaki Resource Report Resource Website |
Murasaki (RRID:SCR_024132) | software library, software resource, software toolkit | Software language-theory based homology detection tool across multiple large genomes. | language-theory based homology detection, multiple large genomes, | is listed by: Debian | PMID:20885980 | Free, Available for download, Freely available, | OMICS_11714 | https://sources.debian.org/src/murasaki/ | SCR_024132 | murasaki | 2026-09-19 12:56:18 | 0 | ||||||
|
Entrez Direct Resource Report Resource Website 10+ mentions |
Entrez Direct (RRID:SCR_024136) | software library, software resource, software toolkit | Software provides access to NCBI's suite of interconnected databases (publication, sequence, structure, gene, variation, expression, etc.) from Unix terminal window. Search terms are entered as command-line arguments. Individual operations are connected with Unix pipes to construct multi-step queries. Selected records can then be retrieved in variety of formats. | access to NCBI's suite of interconnected databases, Unix terminal window, construct multi-step queries, retrive selected records, | is listed by: Debian | https://sources.debian.org/src/ncbi-entrez-direct/ | SCR_024136 | Entrez Direct: E-utilities on the Unix Command Line, EDirect, ncbi-entrez-direct | 2026-09-19 12:56:18 | 13 | |||||||||
|
NJplot Resource Report Resource Website 1+ mentions |
NJplot (RRID:SCR_024137) | software library, software resource, software toolkit | Software tool as tree drawing program to draw any phylogenetic tree expressed in Newick phylogenetic tree format (e.g., the format used by the PHYLIP package).Used for rooting the unrooted trees obtained from parsimony, distance or maximum likelihood tree-building methods. | tree drawing program, draw any phylogenetic tree, Newick phylogenetic tree format, | is listed by: Debian | Free, Available for download, Freely available, | OMICS_04815 | https://sources.debian.org/src/njplot/ | SCR_024137 | njplot | 2026-09-19 12:56:18 | 2 | |||||||
|
Libxdf Resource Report Resource Website |
Libxdf (RRID:SCR_024096) | software library, software resource, software toolkit | Software cross-platform C++ library for loading multimodal, multi-rate signals stored in XDF files. Used in biosignal viewing application SigViewer and the LSL application XDFStreamer. Can also be integrated into other C++ applications. | C++ library, loading multimodal, multi-rate signals, SigViewer, XDFStreamer, biosignal viewing, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/libxdf/, https://xdf-modules.github.io/libxdf/ | SCR_024096 | libxdf, Libxdf � a C++ library for loading XDF files | 2026-09-19 12:56:18 | 0 | ||||||||
|
NanoSV Resource Report Resource Website 1+ mentions |
NanoSV (RRID:SCR_024127) | software resource, software toolkit | Software package that can be used to identify structural genomic variations in long-read sequencing data, such as data produced by Oxford Nanopore Technologies� MinION, GridION or PromethION instruments, or Pacific Biosciences RSII or Sequel sequencers. | identify structural genomic variations, long-read sequencing data, Oxford Nanopore Technologies� MinION, GridION, PromethION, Pacific Biosciences RSII, Sequel sequencers. | is listed by: Debian | PMID:29109544 | Free, Available for download, Freely available, | OMICS_29732 | https://sources.debian.org/src/nanosv/ | SCR_024127 | nanosv | 2026-09-19 12:56:18 | 4 | ||||||
|
CTDConverter Resource Report Resource Website |
CTDConverter (RRID:SCR_024007) | software library, software resource, software toolkit | Software Python scripts to convert CTD files into other formats such as Galaxy, CWL. | Python, scripts to convert CTD files, Galaxy format, CWL format | is listed by: Debian | Free, Available for download, Freely available | https://sources.debian.org/src/ctdconverter/ | SCR_024007 | ctdconverter | 2026-09-19 12:56:17 | 0 | ||||||||
|
NanoPlot Resource Report Resource Website 100+ mentions |
NanoPlot (RRID:SCR_024128) | software library, software resource, software toolkit | Software package as plotting tool for long read sequencing data and alignments. | plotting tool, long read sequencing data and alignments, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/nanoplot/, https://nanoplot.bioinf.be/ | SCR_024128 | nanoplot | 2026-09-19 12:56:18 | 397 | ||||||||
|
OBITools Resource Report Resource Website 10+ mentions |
OBITools (RRID:SCR_024141) | software library, software resource, software toolkit | Software package for analysing NGS data in DNA metabarcoding context. Used to filter and edit sequences while taking into account taxonomic annotation to set up tailor-made analysis pipelines for broad range of DNA metabarcoding applications, including biodiversity surveys or diet analyses. | analysing NGS data, DNA metabarcoding, filter and edit sequences, taxonomic annotation, analysis pipelines for DNA metabarcoding applications, | is listed by: Debian | PMID:25959493 | Free, Available for download, Freely available, | OMICS_32696 | https://sources.debian.org/src/obitools/ | SCR_024141 | obitools | 2026-09-19 12:56:19 | 39 | ||||||
|
FreeImage Resource Report Resource Website 1+ mentions |
FreeImage (RRID:SCR_024022) | software library, software resource, software toolkit | Open Source software library for developers who would like to support popular graphics image formats like PNG, BMP, JPEG, TIFF and others as needed by today's multimedia applications. | support graphics image formats, PNG, BMP, JPEG, TIFF | is listed by: Debian | Free, Available for download, Freely available | https://sources.debian.org/src/freeimage/ | SCR_024022 | freeimage | 2026-09-19 12:56:17 | 2 | ||||||||
|
Orthanc Resource Report Resource Website 1+ mentions |
Orthanc (RRID:SCR_024145) | software library, software resource, software toolkit | Open source lightweight DICOM server for medical imaging.Vendor neutral archive to automate and optimize imaging flows. Can be extended with plugins that provide solutions for teleradiology, digital pathology, or enterprise ready databases. | DICOM server, medical imaging, | is listed by: Debian | PMID:29725964 | Free, Available for download, Freely available, | https://sources.debian.org/src/orthanc/ | SCR_024145 | orthanc | 2026-09-19 12:56:19 | 4 | |||||||
|
NORSnet Resource Report Resource Website |
NORSnet (RRID:SCR_024146) | software library, software resource, software toolkit | Software as neural network based method that focuses on identification of unstructured loops. Trained to distinguish between very long contiguous segments with non-regular secondary structure and well-folded proteins. Trained on predicted information rather than on experimental data. | neural network based method, identification of unstructured loops, distinguish between very long contiguous and well-folded proteins, segments with non-regular secondary structure, | is listed by: Debian | PMID:17658943 | Free, Available for download, Freely available, | OMICS_16034 | https://sources.debian.org/src/norsnet/ | SCR_024146 | norsnet, Norsnet | 2026-09-19 12:56:19 | 0 | ||||||
|
GenomeTester4 Resource Report Resource Website 1+ mentions |
GenomeTester4 (RRID:SCR_024026) | software resource, software toolkit | Software toolkit for performing set operations - union, intersection and complement on k-mer lists. | performing set operations on k-mer lists, | is listed by: Debian | PMID:26640690 | Free, Available for download, Freely available, | OMICS_02363w | https://sources.debian.org/src/genometester/ | SCR_024026 | genometester | 2026-09-19 12:56:17 | 4 |
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