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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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GramAlign Resource Report Resource Website 1+ mentions |
GramAlign (RRID:SCR_024032) | software resource, alignment software, image analysis software, data processing software, software application | Software tool as time efficient progressive Multiple Sequence Alignment algorithm. Sequence distance estimation step is determined by the natural grammar present in nucleotide and amino acid sequences. | Multiple Sequence Alignment, progressive Multiple Sequence Alignment, sequence distance estimation, nucleotide and amino acid sequences, | is listed by: Debian | Free, Freely available | OMICS_05314 | https://sources.debian.org/src/gramalign/ | SCR_024032 | gramalign | 2026-08-06 09:30:18 | 4 | |||||||
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IDeFIX Resource Report Resource Website |
IDeFIX (RRID:SCR_024033) | data analysis software, software application, software resource, data processing software | Software tool for demultiplexing Illumina NGS data. Reports inconsistencies between the raw data and the Sample Sheet, checks for duplicates of indices/ index combinations in the latter and removes unwanted characters from it. Creates an IDeFIX_Report.csv containing the indices/ index combinations from the raw data and their abundance as well as their count in the Sample Sheet and the corresponding Index ID(s). | demultiplexing Illumina NGS data, reports inconsistencies, checks for duplicates of indices, removes unwanted characters, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/idefix/ | SCR_024033 | idefix | 2026-08-06 09:30:14 | 0 | ||||||||
|
GraphMap2 Resource Report Resource Website 10+ mentions |
GraphMap2 (RRID:SCR_024035) | data analysis software, software application, software resource, data processing software | Software tool as splice aware RNA-seq mapper for long reads produced by Pacific Biosciences and Oxford Nanopore devices | splice aware RNA-seq mapper, long reads, Pacific Biosciences, Oxford Nanopore, | is listed by: Debian | PMID:27079541 | Free, Available for download, Freely available, | https://sources.debian.org/src/graphmap2/ | SCR_024035 | graphmap2 | 2026-08-06 09:30:18 | 21 | |||||||
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PCMA Resource Report Resource Website |
PCMA (RRID:SCR_024156) | software resource, alignment software, image analysis software, data processing software, software application | Software tool for multiple sequence alignment based on profile consistency. Used to construct multiple sequence alignment given set of protein sequences. | multiple sequence alignment, profile consistency, construct multiple sequence alignment, protein sequences, | is listed by: Debian | PMID:12584134 | Free, Available for download, Freely available, | OMICS_14997 | https://sources.debian.org/src/pcma/ | SCR_024156 | pcma, Profile Consistency Multiple Sequence Alignment | 2026-08-06 09:30:20 | 0 | ||||||
|
PartitionFinder Resource Report Resource Website 500+ mentions |
PartitionFinder (RRID:SCR_024157) | data analysis software, software application, software resource, data processing software | Software Python program to discover optimal partitioning schemes for DNA sequences.Used for simultaneously choosing partitioning schemes and models of molecular evolution for phylogenetic analyses of DNA, protein, and morphological data. | discover optimal partitioning schemes, DNA sequences, simultaneously choosing partitioning schemes and models, phylogenetic analyses of DNA, phylogenetic analyses of protein, phylogenetic analyses of morphological data, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/partitionfinder/ | SCR_024157 | partitionfinder, PartitionFinder 2 | 2026-08-06 09:30:16 | 704 | ||||||||
|
BioMAJ Resource Report Resource Website |
BioMAJ (RRID:SCR_023983) | software application, software resource, workflow software, data processing software | Software workflow engine dedicated to data synchronization and processing. Software automates the update cycle and the supervision of the locally mirrored databank repository. | workflow engine, data synchronization and processing, | is listed by: Debian | Free, Available for download, Freely available | OMICS_21717 | https://sources.debian.org/src/biomaj3/, http://genouest.github.io/biomaj/ | SCR_023983 | BioMAJ3, BIOlogie Mise A Jour, biomaj3 | 2026-08-06 09:30:14 | 0 | |||||||
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TM-align Resource Report Resource Website 1+ mentions |
TM-align (RRID:SCR_024390) | data analysis software, software application, software resource, data processing software | Software tool for protein structure alignment based on TM-score.Used to identify structural alignment between protein pairs that combines the TM-score rotation matrix and Dynamic Programming. Used for sequence independent protein structure comparisons. | protein structure alignment, TM-score, identify structural alignment between protein pairs, sequence independent protein structure comparisons, | is listed by: Debian | PMID:15849316 | Free, Available for download, Freely available, | OMICS_03646 | https://sources.debian.org/src/tm-align/ | SCR_024390 | 2026-08-06 09:30:18 | 9 | |||||||
|
toil Resource Report Resource Website 1+ mentions |
toil (RRID:SCR_024391) | data management software, software application, software resource | Software pipeline management system, written in Python. Enables reproducible, open source, big biomedical data analyses. | management system, Python, biomedical data analyses, | is listed by: Debian | PMID:28398314 | Free, Available for download, Freely available, | OMICS_25666 | https://sources.debian.org/src/toil/ | SCR_024391 | 2026-08-06 09:30:18 | 2 | |||||||
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PAIPline Resource Report Resource Website |
PAIPline (RRID:SCR_024151) | data analysis software, software application, software resource, data processing software | Software Python program to search for pathogen nucleic acid sequences in NGS datasets.Used for pathogen identification in metagenomic and clinical next generation sequencing samples. | Python program, pathogen nucleic acid sequences in NGS datasets search, pathogen identification, metagenomic and clinical next generation sequencing samples, | is listed by: Debian | PMID:30423069 | Free, Available for download, Freely available, | https://sources.debian.org/src/paipline/ | SCR_024151 | 2026-08-06 09:30:16 | 0 | ||||||||
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pipasic Resource Report Resource Website |
pipasic (RRID:SCR_024165) | data analysis software, software application, software resource, data processing software | Software tool for similarity and expression correction for strain level identification and quantification in metaproteomics. Peptide intensity weighted proteome abundance similarity correction tool to correct identification and spectral counting based quantification results. Pipasic has distinct advantages over approaches only regarding unique peptides or aggregating results to the lowest common ancestor. | similarity and expression correction, strain level identification and quantification, metaproteomics, peptide intensity weighted proteome abundance similarity, correct identification and spectral counting, quantification results, peptide similarity estimation and expression level weighting within non-negative lasso framework, | is listed by: Debian | PMID:24931978 | Free, Available for download, Freely available, | https://sources.debian.org/src/pipasic/ | SCR_024165 | 2026-08-06 09:30:17 | 0 | ||||||||
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PlasmidID Resource Report Resource Website 1+ mentions |
PlasmidID (RRID:SCR_024166) | data analysis software, software application, software resource, data processing software | Software mapping based, assembly assisted plasmid identification tool that analyzes and gives graphic solution for plasmid identification. Computational pipeline implemented in BASH that maps Illumina reads over plasmid database sequences. | plasmid identification, analyzes and gives graphic solution for plasmid identification, maps Illumina reads, plasmid database sequences, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/plasmidid/, https://github.com/BU-ISCIII/plasmidID/wiki | SCR_024166 | plasmidid | 2026-08-06 09:30:20 | 4 | ||||||||
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kineticsTools Resource Report Resource Website 1+ mentions |
kineticsTools (RRID:SCR_024049) | data analysis software, software application, software resource, data processing software | Software tools for detecting DNA modifications from single molecule, real-time sequencing data. This tool implements the P_ModificationDetection module in SMRT� Portal, used by the RS_Modification_Detection and RS_Modifications_and_Motif_Detection protocol. | detecting DNA modifications from single molecule, real-time sequencing data, | is listed by: Debian | Free, Available for download, Freely available, | OMICS_18309 | https://sources.debian.org/src/kineticstools/ | SCR_024049 | kineticstools | 2026-08-06 09:30:18 | 3 | |||||||
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Insight Toolkit Resource Report Resource Website 10+ mentions |
Insight Toolkit (RRID:SCR_024040) | image analysis software, software application, software resource, data processing software | Open source, software cross-platform library that provides suite of software tools for image analysis.ITK builds on proven, spatially-oriented architecture for processing, segmentation, and registration of scientific images in two, three, or more dimensions. | image analysis, 2D, 3D, images | is listed by: Debian | Free, Freely available | https://sources.debian.org/src/insighttoolkit4/, https://github.com/InsightSoftwareConsortium/ITK | SCR_024040 | ITK, insighttoolkit4 | 2026-08-06 09:30:18 | 14 | ||||||||
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resfinder Resource Report Resource Website 500+ mentions |
resfinder (RRID:SCR_024314) | data analysis software, software application, software resource, data processing software | Software tool identifies acquired antimicrobial resistance genes in total or partial sequenced isolates of bacteria. Used for identification of acquired antimicrobial resistance genes in whole-genome data. | acquired antimicrobial resistance genes identification, total or partial sequenced isolates, identification of acquired antimicrobial resistance genes, whole genome data, | is listed by: Debian | PMID:22782487 | Free, Available for download, Freely available, | https://sources.debian.org/src/resfinder/ | SCR_024314 | ResFinder | 2026-08-06 09:30:18 | 832 | |||||||
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Ngila Resource Report Resource Website |
Ngila (RRID:SCR_024133) | software resource, alignment software, image analysis software, data processing software, software application | Software alignment program that can align pairs of sequences using logarithmic and affine gap penalties. | alignment program, align pairs of sequences, logarithmic and affine gap penalties, | is listed by: Debian | PMID:17387111 | Free, Available for download, Freely available, | OMICS_03695 | https://sources.debian.org/src/ngila/ | SCR_024133 | ngila | 2026-08-06 09:30:16 | 0 | ||||||
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VarMatch Resource Report Resource Website 1+ mentions |
VarMatch (RRID:SCR_024375) | data analysis software, software application, software resource, data processing software | Software tool for variant matching problem.Used for robust matching of small variant datasets using flexible scoring schemes | variant matching, matching of small variant datasets, flexible scoring schemes, | is listed by: Debian | PMID:28011786 | Free, Available for download, Freely available, | OMICS_14435 | https://sources.debian.org/src/varmatch/ | SCR_024375 | varmatch | 2026-08-06 09:30:21 | 1 | ||||||
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NextSV Resource Report Resource Website |
NextSV (RRID:SCR_024134) | data analysis software, software application, software resource, data processing software | Software tool for automated structrual variation detection from long-read sequencing using state-of-the-art tools. NextSV3 uses Minimap2 to do read mapping and uses two state-of-the-art SV callers (Sniffles and cuteSV) to do SV calling. | structrual variation detection from long-read sequencing, structrual variation detection, long-read sequencing, | is listed by: Debian | DOI:10.1101/092544 | Free, Available for download, Freely available, | OMICS_30332 | https://sources.debian.org/src/nextsv/ | SCR_024134 | nextsv, NextSV3 | 2026-08-06 09:30:16 | 0 | ||||||
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Nextflow Resource Report Resource Website 100+ mentions |
Nextflow (RRID:SCR_024135) | software application, software resource, workflow software, data processing software | Software workflow manager that enables development of portable and reproducible workflows.Supports deploying workflows on variety of execution platforms including local, HPC schedulers, AWS Batch, Google Cloud Life Sciences, and Kubernetes. Provides support to manage workflow dependencies through built-in support for Conda, Spack, Docker, Podman, Singularity, Modules, and more. | development of portable and reproducible workflows, deploying workflows, manage workflow dependencies, |
is used by: cutandrun is listed by: Debian works with: NEXT-scASV |
PMID:28398311 | Free, Available for download, Freely available, | https://sources.debian.org/src/nextflow/, https://nextflow.io/ | SCR_024135 | nextflow | 2026-08-06 09:30:20 | 132 | |||||||
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VADR Resource Report Resource Website 1+ mentions |
VADR (RRID:SCR_024377) | data analysis software, software application, software resource, data processing software | Software suite of tools for classifying and analyzing sequences homologous to set of reference models of viral genomes or gene families. | classifying and analyzing sequences, sequences homologous to set of reference models, viral genomes reference models, gene families reference models, | is listed by: Debian | PMID:35441162 | Free, Available for download, Freely available, | https://sources.debian.org/src/vadr/ | SCR_024377 | ushahidi | 2026-08-06 09:30:18 | 1 | |||||||
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FISH Resource Report Resource Website 1+ mentions |
FISH (RRID:SCR_024378) | data analysis software, software application, software resource, data processing software | Software tool for identifying regions of common ancestry between genome maps. Used for identification and statistical evaluation of segmental homologies in comparative maps. | identifying regions of common ancestry, genome maps, identification and statistical evaluation, segmental homologies in comparative maps, | is listed by: Debian | PMID:12855440 | Free, Available for download, Freely available, | OMICS_11724 | https://sources.debian.org/src/unc-fish/ | SCR_024378 | 2026-08-06 09:30:18 | 1 |
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