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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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TM-align Resource Report Resource Website 1+ mentions |
TM-align (RRID:SCR_024390) | data processing software, data analysis 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 | 2026-07-31 09:29:27 | 9 | |||||||
|
toil Resource Report Resource Website 1+ mentions |
toil (RRID:SCR_024391) | software resource, software application, data management software | 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 | 2026-07-31 09:29:25 | 2 | |||||||
|
PAIPline Resource Report Resource Website |
PAIPline (RRID:SCR_024151) | data processing software, data analysis 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 | 2026-07-31 09:29:17 | 0 | ||||||||
|
pipasic Resource Report Resource Website |
pipasic (RRID:SCR_024165) | data processing software, data analysis 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 | 2026-07-31 09:29:22 | 0 | ||||||||
|
PlasmidID Resource Report Resource Website 1+ mentions |
PlasmidID (RRID:SCR_024166) | data processing software, data analysis 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 | plasmidid | 2026-07-31 09:29:18 | 4 | ||||||||
|
kineticsTools Resource Report Resource Website 1+ mentions |
kineticsTools (RRID:SCR_024049) | data processing software, data analysis 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 | kineticstools | 2026-07-31 09:29:18 | 3 | |||||||
|
ChromImpute Resource Report Resource Website |
ChromImpute (RRID:SCR_023990) | software resource, software application, simulation software | Software tool for large scale systematic epigenome imputation. ChromImpute takes existing compendium of epigenomic data and uses it to predict signal tracks for mark-sample combinations not experimentally mapped or to generate a potentially more robust version of data sets that have been mapped experimentally. | systematic epigenome imputation, epigenomic data, predict signal tracks, mark-sample combinations, not experimentally mapped data, | is listed by: Debian | Free, Available for download, Freely available | OMICS_11185 | https://sources.debian.org/src/chromimpute/ | SCR_023990 | chromimpute | 2026-07-31 09:29:14 | 0 | |||||||
|
Insight Toolkit Resource Report Resource Website 10+ mentions |
Insight Toolkit (RRID:SCR_024040) | image analysis software, software application, data processing software, software resource | 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 | 2026-07-31 09:29:17 | 14 | ||||||||
|
InSilicoSeq Resource Report Resource Website 1+ mentions |
InSilicoSeq (RRID:SCR_024041) | software resource, software application, simulation software | Software tool as sequencing simulator producing realistic Illumina reads. Primarily intended for simulating metagenomic samples, it can also be used to produce sequencing data from a single genome. | producing realistic Illumina reads, simulating metagenomic samples, | is listed by: Debian | PMID:30016412 | Free, Available for download, Freely available, | OMICS_31218 | https://sources.debian.org/src/insilicoseq/, https://insilicoseq.readthedocs.io/en/latest/ | SCR_024041 | insilicoseq, InSilicoSeq- A sequencing simulator | 2026-07-31 09:29:14 | 7 | ||||||
|
resfinder Resource Report Resource Website 500+ mentions |
resfinder (RRID:SCR_024314) | data processing software, data analysis 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 | ResFinder | 2026-07-31 09:29:21 | 832 | |||||||
|
Ngila Resource Report Resource Website |
Ngila (RRID:SCR_024133) | image analysis software, alignment software, software application, software resource, data processing software | 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 | 2026-07-31 09:29:17 | 0 | ||||||
|
VarMatch Resource Report Resource Website 1+ mentions |
VarMatch (RRID:SCR_024375) | data processing software, data analysis 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 | varmatch | 2026-07-31 09:29:26 | 1 | ||||||
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NextSV Resource Report Resource Website |
NextSV (RRID:SCR_024134) | data processing software, data analysis 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 | nextsv, NextSV3 | 2026-07-31 09:29:17 | 0 | ||||||
|
Nextflow Resource Report Resource Website 100+ mentions |
Nextflow (RRID:SCR_024135) | workflow software, software application, data processing software, software resource | 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 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 | 2026-07-31 09:29:21 | 132 | |||||||
|
VADR Resource Report Resource Website 1+ mentions |
VADR (RRID:SCR_024377) | data processing software, data analysis 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 | ushahidi | 2026-07-31 09:29:24 | 1 | |||||||
|
FISH Resource Report Resource Website 1+ mentions |
FISH (RRID:SCR_024378) | data processing software, data analysis 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 | 2026-07-31 09:29:22 | 1 | |||||||
|
Epigrass Resource Report Resource Website |
Epigrass (RRID:SCR_024016) | software resource, software application, simulation software | Software Python library aimed at making the simulation of metapopulation models. Software tool to study disease spread in complex networks.Used to help designing and simulating network-epidemic models with any kind of node behavior. | simulation of metapopulation models, simulating network-epidemic models, study disease spread in complex networks, | is listed by: Debian | PMID:18302744 | Free, Available for download, Freely available | OMICS_19988 | https://sources.debian.org/src/epigrass/ | SCR_024016 | epigrass, Epidemiological Geo-referenced Analysis and Simulation system | 2026-07-31 09:29:14 | 0 | ||||||
|
DNApi Resource Report Resource Website |
DNApi (RRID:SCR_024009) | software resource, software application, simulation software | Software de novo adapter prediction algorithm for small RNA sequencing data. | prediction algorithm, small RNA sequencing data, | is listed by: Debian | PMID:27736901 | Free, Available for download, Freely available | OMICS_13264 | https://sources.debian.org/src/dnapi/ | SCR_024009 | dnapi | 2026-07-31 09:29:14 | 0 | ||||||
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omegaMap Resource Report Resource Website 10+ mentions |
omegaMap (RRID:SCR_024143) | data processing software, data analysis 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 | omegamap | 2026-07-31 09:29:17 | 32 | ||||||
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OpenEMR Resource Report Resource Website 1+ mentions |
OpenEMR (RRID:SCR_024144) | software resource, software application, data management software | 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 | openemr | 2026-07-31 09:29:21 | 1 |
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