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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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TM-align Resource Report Resource Website 10+ mentions |
TM-align (RRID:SCR_024390) | data analysis software, data processing software, software application, software resource | 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 | SciCrunch Registry | 2026-10-17 01:31:39 | 15 | |||||||
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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 | SciCrunch Registry | 2026-10-17 01:32:43 | 2 | |||||||
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PAIPline Resource Report Resource Website |
PAIPline (RRID:SCR_024151) | data analysis software, data processing software, software application, software resource | 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 | SciCrunch Registry | 2026-10-17 01:31:40 | 0 | ||||||||
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pipasic Resource Report Resource Website |
pipasic (RRID:SCR_024165) | data analysis software, data processing software, software application, software resource | 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 | SciCrunch Registry | 2026-10-17 01:31:40 | 0 | ||||||||
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PlasmidID Resource Report Resource Website 1+ mentions |
PlasmidID (RRID:SCR_024166) | data analysis software, data processing software, software application, software resource | 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 | SciCrunch Registry | plasmidid | 2026-10-17 01:32:03 | 7 | ||||||||
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kineticsTools Resource Report Resource Website 1+ mentions |
kineticsTools (RRID:SCR_024049) | data analysis software, data processing software, software application, software resource | 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 | SciCrunch Registry | kineticstools | 2026-10-17 01:32:02 | 3 | |||||||
|
resfinder Resource Report Resource Website 500+ mentions |
resfinder (RRID:SCR_024314) | data analysis software, data processing software, software application, software resource | 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 | SciCrunch Registry | ResFinder | 2026-10-17 01:32:04 | 969 | |||||||
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Ngila Resource Report Resource Website |
Ngila (RRID:SCR_024133) | alignment software, data processing software, image analysis software, software application, software resource | 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 | SciCrunch Registry | ngila | 2026-10-17 01:32:03 | 0 | ||||||
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VarMatch Resource Report Resource Website 1+ mentions |
VarMatch (RRID:SCR_024375) | data analysis software, data processing software, software application, software resource | 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 | SciCrunch Registry | varmatch | 2026-10-17 01:31:41 | 1 | ||||||
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NextSV Resource Report Resource Website |
NextSV (RRID:SCR_024134) | data analysis software, data processing software, software application, software resource | 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 | SciCrunch Registry | nextsv, NextSV3 | 2026-10-17 01:31:38 | 0 | ||||||
|
Nextflow Resource Report Resource Website 100+ mentions |
Nextflow (RRID:SCR_024135) | data processing software, software application, software resource, workflow 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 used by: variantbenchmarking 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 | SciCrunch Registry | nextflow | 2026-10-17 01:32:42 | 138 | |||||||
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VADR Resource Report Resource Website 1+ mentions |
VADR (RRID:SCR_024377) | data analysis software, data processing software, software application, software resource | 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 | SciCrunch Registry | ushahidi | 2026-10-17 01:32:04 | 1 | |||||||
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FISH Resource Report Resource Website 1+ mentions |
FISH (RRID:SCR_024378) | data analysis software, data processing software, software application, software resource | 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 | SciCrunch Registry | 2026-10-17 01:31:39 | 1 | |||||||
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TopHat-Recondition Resource Report Resource Website |
TopHat-Recondition (RRID:SCR_024383) | data processing software, software application, software resource | Software tool as post-processor for TopHat unmapped reads that restores read information in the proper format.Enables downstream software to process plethora of BAM files written by TopHat. | post-processor for TopHat unmapped reads, restore read information in the proper format, process plethora of BAM files written by TopHat, | is listed by: Debian | PMID:27142976 | Free, Available for download, Freely available, | https://sources.debian.org/src/tophat-recondition/ | SCR_024383 | SciCrunch Registry | 2026-10-17 01:31:41 | 0 | ||||||||
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omegaMap Resource Report Resource Website 10+ mentions |
omegaMap (RRID:SCR_024143) | data analysis software, data processing software, software application, software resource | Software tool for detecting natural selection and recombination in DNA or RNA sequences. | detecting natural selection and recombination, DNA sequences, RNA sequences | is listed by: Debian | DOI:10.1534/genetics.105.044917 | Free, Available for download, Freely available, | OMICS_31719 | https://sources.debian.org/src/omegamap/ | SCR_024143 | SciCrunch Registry | omegamap | 2026-10-17 01:31:38 | 32 | ||||||
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OpenEMR Resource Report Resource Website 1+ mentions |
OpenEMR (RRID:SCR_024144) | data management software, software application, software resource | Open source software for electronic health records and medical practice management solution. | electronic health records, medical practice management, | is listed by: Debian | Free, Available for download, Freely available, | https://github.com/openemr/openemr | https://sources.debian.org/src/openemr/ | SCR_024144 | SciCrunch Registry | openemr | 2026-10-17 01:32:42 | 1 | |||||||
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Tombo Resource Report Resource Website 10+ mentions |
Tombo (RRID:SCR_024388) | data analysis software, data processing software, software application, software resource | Software suite of tools for identification of modified nucleotides from nanopore sequencing data.Used also for analysis and visualization of raw nanopore signal. | identification of modified nucleotides, nanopore sequencing data, analysis and visualization of raw nanopore signal, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/tombo/ | SCR_024388 | SciCrunch Registry | ont-tombo | 2026-10-17 01:31:41 | 18 | ||||||||
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NW-align Resource Report Resource Website |
NW-align (RRID:SCR_024138) | alignment software, data access protocol, data processing software, image analysis software, software application, software resource, web service | Software tool as alignment program for protein sequence-to-sequence alignments based on the standard Needleman-Wunsch dynamic programming algorithm. | protein sequence-to-sequence alignments, standard Needleman-Wunsch dynamic programming algorithm, | is listed by: Debian | Free, Freely available, | https://sources.debian.org/src/nw-align/ | SCR_024138 | SciCrunch Registry | nw-align | 2026-10-17 01:31:40 | 0 | ||||||||
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MicrobeGPS Resource Report Resource Website |
MicrobeGPS (RRID:SCR_024112) | data analysis software, data processing software, software application, software resource | Software tool for analysis of metagenomic sequencing data.Used to profile composition of metagenomic communities. Calculates quality metrics for estimated candidates and allows the user to identify false candidates. | metagenomic sequencing data analysis, profile composition of metagenomic communities, identify false candidates, | is listed by: Debian | PMID:25643362 | Free, Available for download, Freely available, | OMICS_17085 | https://sources.debian.org/src/microbegps/ | SCR_024112 | SciCrunch Registry | microbegps | 2026-10-17 01:31:38 | 0 | ||||||
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surankco Resource Report Resource Website 1+ mentions |
surankco (RRID:SCR_024355) | simulation software, software application, software resource | Machine learning based software to score and rank contigs from de novo assemblies of next generation sequencing data. It trains with alignments of contigs with known reference genomes and predicts scores and ranking for contigs which have no related reference genome yet. | score and rank contigs, de novo assemblies of next generation sequencing data, | is listed by: Debian | PMID:26224355 | Free, Available for download, Freely available, | OMICS_09480 | https://sources.debian.org/src/surankco/ | SCR_024355 | SciCrunch Registry | 2026-10-17 01:31:41 | 1 |
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