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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
GENERECON Resource Report Resource Website 1+ mentions |
GENERECON (RRID:SCR_009195) | GENERECON | software application, software resource | Software application for linkage disequilibrium mapping using coalescent theory. It is based on a Bayesian Markov-chain Monte Carlo (MCMC) method for fine-scale linkage-disequilibrium gene mapping using high-density marker maps. GeneRecon explicitly models the genealogy of a sample of the case chromosomes in the vicinity of a disease locus. Given case and control data in the form of genotype or haplotype information, it estimates a number of parameters, most importantly, the disease position. (entry from Genetic Analysis Software) | gene, genetic, genomic, c++, unix, linux, macos, ms-windows, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
nlx_154338, biotools:generecon | https://bio.tools/generecon | SCR_009195 | 2026-07-26 09:04:45 | 1 | ||||||||
|
HTR Resource Report Resource Website 1+ mentions |
HTR (RRID:SCR_009241) | HTR | software application, software resource | Software application for haplotype association mapping using unrelated individuals; fixed and sliding window analysis; overall tests and tests for individual haplotype effects (entry from Genetic Analysis Software) | gene, genetic, genomic, c++, bash shell, ms-windows, unix, solaris, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
nlx_154402, biotools:htr | https://bio.tools/htr | SCR_009241 | Haplotype Trend Regression | 2026-07-26 09:04:46 | 1 | |||||||
|
ImageVis3D Resource Report Resource Website 10+ mentions |
ImageVis3D (RRID:SCR_009566) | ImageVis3D | software application, software resource, data processing software | A new volume rendering program developed by the NIH/NCRR Center for Integrative Biomedical Computing (CIBC). The main design goals of ImageVis3D are: simplicity, scalability, and interactivity. Simplicity is achieved with a new user interface that gives an unprecedented level of flexibility (as shown in the images). Scalability and interactivity for ImageVis3D mean that both on a notebook computer as well as on a high end graphics workstation, the user can interactively explore terabyte sized data sets. Finally, the open source nature as well as the strict component-by-component design allow developers not only to extend ImageVis3D itself but also reuse parts of it, such as the rendering core. This rendering core, for instance, is planned to replace the volume rendering subsystems in many applications at the SCI Institute and with their collaborators. | magnetic resonance, rendering |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian has parent organization: University of Utah; Utah; USA |
NCRR P41-RR12553-15; DOE DEFC0206ER25781 |
Free, Available for download, Freely available | nlx_155776 | http://www.nitrc.org/projects/imagevis3d, https://sources.debian.org/src/imagevis3d/ | SCR_009566 | 2026-07-26 09:04:53 | 10 | ||||||
|
Trimmomatic Resource Report Resource Website 10000+ mentions |
Trimmomatic (RRID:SCR_011848) | Trimmomatic | software application, software resource, data processing software | Software Java pipeline for trimming tasks for Illumina paired end and single ended data. Flexible Trimmer for Illumina Sequence Data. Pair aware preprocessing tool optimized for Illumina next generation sequencing data. Includes several processing steps for read trimming and filtering. Operating systems Unix/Linux, Mac OS, Windows. | trimming, task, paired, end, single, data, next, generation, sequencing, filtering, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: shovill |
BLE/BMELV Verbundprojekt ; BMBF |
PMID:24695404 DOI:10.1093/bioinformatics/btu170 |
biotools:trimmomatic, OMICS_01097 | https://omictools.com/trimmomatic-tool, https://bio.tools/trimmomatic, https://sources.debian.org/src/trimmomatic/ | SCR_011848 | Trimmomatic v 0.32 | 2026-07-26 09:05:31 | 21028 | |||||
|
xia2 pipeline Resource Report Resource Website 10+ mentions |
xia2 pipeline (RRID:SCR_015746) | software application, software resource, data processing software | Data processing software that performs X-ray diffraction data processing. It handles multi-pass, multi-wavelength data sets and supports remote access to synchrotron facilities. | xray, diffraction, data processing, synchrotron, mmulti-pass, multi-wavelength, bio.tools |
is listed by: bio.tools is listed by: Debian |
PMID:23793152 | Open Source, Available for download | biotools:xia2 | https://bio.tools/xia2 | SCR_015746 | 2026-07-26 09:06:36 | 34 | |||||||
|
rnaQUAST Resource Report Resource Website 1+ mentions |
rnaQUAST (RRID:SCR_016994) | software application, software resource, data processing software | Software tool for evaluating RNA-Seq assembly quality and benchmarking transcriptome assemblers using reference genome and gene database. Capable to estimate gene database coverage by raw reads and de novo quality assessment using third party software. | evaluation, quality, RNA-Seq, assembly, data, transcriptome, assembler, reference, genome, gene, database, raw, read, , bio.tools |
uses: BUSCO is listed by: Debian is listed by: bio.tools is related to: rnaSPAdes is related to: Python Programming Language is related to: SPAdes |
EMC Research and Development Department ; St. Petersburg State University ; Russia |
PMID:27153654 | Free, Available for download, Freely available | biotools:rnaQUASt | https://bio.tools/rnaQUAST | SCR_016994 | 2026-07-26 09:06:52 | 3 | ||||||
|
Porechop Resource Report Resource Website 1000+ mentions |
Porechop (RRID:SCR_016967) | software application, software resource, data processing software | Software tool for finding and removing adapters from Oxford Nanopore reads. | finding, removing, adapter, Oxford Nanopore, read, sequencing, data |
is listed by: Debian is listed by: OMICtools |
Free, Available for download, Freely available | OMICS_17306 | https://sources.debian.org/src/porechop/ | SCR_016967 | 2026-07-26 09:06:53 | 1100 | ||||||||
|
PASTEClassifier Resource Report Resource Website 10+ mentions |
PASTEClassifier (RRID:SCR_017645) | PASTEC | software application, software resource, data processing software | Software tool for automatic transposable element classification. Used for searching for structural features and similarity to classify transposable elements. | Automatic, transposable, element, classification, bio.tools, bio.tools |
is listed by: Debian is listed by: bio.tools |
French National Research Agency | PMID:24786468 | Free, Available for download, Freely available | biotools:PAStEClassifier | https://urgi.versailles.inra.fr/download/repet/PASTEClassifier-1.0.tar.gz, https://bio.tools/repet, https://bio.tools/PASTEClassifier | SCR_017645 | Pseudo Agent System for Transposable Elements Classification, PASTEC | 2026-07-26 09:07:03 | 11 | ||||
|
Sniffles Resource Report Resource Website 50+ mentions |
Sniffles (RRID:SCR_017619) | software application, software resource, data processing software | Software tool as structural variation caller using third generation sequencing (PacBio or Oxford Nanopore). It detects all types of SVs (10bp+) using evidence from split-read alignments, high-mismatch regions, and coverage analysis. Used to avoid single molecule long read sequencing high error rates. | Structural, variation, caller, third, generation, sequencing, SV, split, read, alignment, mismatch, region, analysis, error, bio.tools |
is listed by: bio.tools is listed by: Debian |
NHGRI R01 HG006677; NHGRI UM1 HG008898 |
PMID:29713083 | Free, Available for download, Freely available | biotools:sniffles | https://bio.tools/sniffles | SCR_017619 | 2026-07-26 09:07:02 | 59 | ||||||
|
MEGAHIT Resource Report Resource Website 1000+ mentions |
MEGAHIT (RRID:SCR_018551) | software application, software resource, data processing software | Software tool as Next Generation Sequencing assembler. Optimized for metagenomes, but also works well on generic single genome assembly (small or mammalian size) and single cell assembly. Can assemble genome sequences from metagenomic datasets of hundreds of Giga base-pairs in time and memory efficient manner on single server. | NGS metagenome, Next Generation Sequencing assembler, metagenome, genome assembly, genome sequence, metagenomic dataset, giga base pairs, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools |
Hong Kong GRF ; Innovation and Technology Fund |
PMID:25609793 PMID:27012178 |
Free, Available for download, Freely available | OMICS_07234, biotools:megahit | https://bio.tools/megahit, https://sources.debian.org/src/megahit/ | SCR_018551 | MEGAHIT v0.1 | 2026-07-26 09:07:16 | 1451 | |||||
|
gffread Resource Report Resource Website 10+ mentions |
gffread (RRID:SCR_018965) | software application, software resource, data processing software | Open source software tool to manipulate files in GFF format. Used to convert, sort, filter, transform, or cluster genomic features. | Gene annotation, transcriptome analysis, GFF file format, convert, sort, filter, transform, cluster genomic feature |
is listed by: Debian is listed by: OMICtools |
DOI:10.12688/f1000research.23297.1 | Free, Available for download, Freely available | OMICS_28050 | https://github.com/gpertea/gffread, https://sources.debian.org/src/gffread/ | SCR_018965 | General Feature Format Read, GFF Read | 2026-07-26 09:07:18 | 26 | ||||||
|
Pychopper Resource Report Resource Website 10+ mentions |
Pychopper (RRID:SCR_018966) | software application, software resource, data processing software | Software tool to identify, orient and trim full length Nanopore cDNA reads. Able to rescue fused reads. | cDNA reads, Nanopore cDNA reads, identify reads, orient reads, trim full length reads, Nanopore reads, rescue fused reads |
is listed by: Debian is related to: Oxford Nanopore Technologies |
Free, Freely available | https://sources.debian.org/src/python3-pychopper/ | SCR_018966 | Pychopper v2 | 2026-07-26 09:07:25 | 26 | ||||||||
|
rna-stability Resource Report Resource Website 1+ mentions |
rna-stability (RRID:SCR_019259) | software application, software resource, data processing software | Software tool as parallel processing framework for large scale generation of secondary RNA structures and folding statistics for transcriptome of any species. | Secondary RNA structures generation, large scale generation, RNA structures, transcriptome folding statistics, , bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Freely available | biotools:rna-stability | https://bio.tools/rna-stability | SCR_019259 | 2026-07-26 09:07:23 | 1 | ||||||||
|
TGS-GapCloser Resource Report Resource Website 10+ mentions |
TGS-GapCloser (RRID:SCR_017633) | software application, software resource, data processing software | Software tool that uses long reads to enhance genome assembly. Fast and accurate gap closing software tool that uses low coverage of error-prone long reads generated by third generation sequence techniques (Pacbio, Oxford Nanopore, etc.) or preassembled contigs for large genomes. | Error, prone, third, generation, sequencing, long, read, gap, closing, genome, assembly, contig, bio.tools |
is listed by: Debian is listed by: bio.tools |
Free, Available for download, Freely available | biotools:tGS-GapCloser | https://bio.tools/TGS-GapCloser | SCR_017633 | 2026-07-26 09:07:08 | 35 | ||||||||
|
mosdepth Resource Report Resource Website 10+ mentions |
mosdepth (RRID:SCR_018929) | software application, software resource, data processing software | Software command line tool for rapidly calculating genome wide sequencing coverage. Measures depth from BAM or CRAM files at either each nucleotide position in genome or for sets of genomic regions. Used for fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing quick coverage calculation for genomes and exomes. | Calculating genome, wide sequencing coverage, depth measurement, BAM file, CRAM file, nucleotide position, genome, genomic region set, WGS exom, targeted sequencing, coverage calculation, exom, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
NHGRI R01 HG006693; NHGRI R01 HG009141; NIGMS R01 GM124355; NCI U24 CA209999 |
PMID:29096012 | Free, Available for download, Freely available | OMICS_20873, biotools:mosdepth | https://bio.tools/mosdepth, https://sources.debian.org/src/mosdepth/ | SCR_018929 | 2026-07-26 09:07:18 | 38 | ||||||
|
parSMURF Resource Report Resource Website 1+ mentions |
parSMURF (RRID:SCR_017560) | software application, software resource, data processing software | Open source software package as high performance computing imbalance aware machine learning tool for genome wide detection of pathogenic variants. | High, performance, computing, imbalance, aware, machine, learning, genome, wide, detection, pathogenic, variant, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Available for download, Freely available | biotools:parsmurf | https://bio.tools/parsmurf | SCR_017560 | 2026-07-26 09:07:01 | 1 | ||||||||
|
EHRtemporalVariability Resource Report Resource Website 1+ mentions |
EHRtemporalVariability (RRID:SCR_018663) | software application, software resource, data processing software | Software R package for delineating temporal dataset shifts in electronic health records. Functions to delineate temporal dataset shifts in electronic health records through projection and visualization of dissimilarities among data temporal batches.Enables exploration and identification of dataset shifts, contributing to broadly examine and repurpose large, longitudinal datasets. Used to help ensure reliable data reuse to biomedical data users. | Delineating temporal data set shift, data set shift, electronic health record, temporal variability, delineate temporal data set shift, data dissimilarities, reliable data reuse, examine data set, biomedical data reuse, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: CRAN is related to: Shiny |
DOI:10.1101/2020.04.07.20056564 | Free, Available for download, Freely available | biotools:ehrtemporalvariability | https://cran.r-project.org/web/packages/EHRtemporalVariability/readme/README.html, https://bio.tools/ehrtemporalvariability | SCR_018663 | Electronic Health Records temporal variability | 2026-07-26 09:07:16 | 3 | ||||||
|
SimVascular Resource Report Resource Website 50+ mentions |
SimVascular (RRID:SCR_002686) | software application, simulation software, software resource | Open source software suite for cardiovascular simulation. It includes code for reading 3D images, segmenting structures, generating models and meshes, and modeling blood flow in deformable vessels. The suite also includes tools for physiologic boundary conditions, fluid structure interaction, and an accurate and efficient finite element Navier-Stokes solver. Commercial components have been used in the simulation process, and for these components, the project attempts to provide interfaces that allow substitution of open source components. The SimVascular project is derived from the ASPIRE2 software project and includes modified portions of PHASTA from RPI/SCOREC. | simulation software, fluid dynamics, blood flow, cardiovascular, image-based geometric modeling, image segmentation, mesh generation, vascular, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Simtk.org |
PMID:31446517 | Free, Available for download, Freely available | nif-0000-23311, BioTools:SimVascular, biotools:SimVascular | https://bio.tools/SimVascular, https://bio.tools/SimVascular, https://bio.tools/SimVascular | SCR_002686 | SimVascular: Cardiovascular Modeling and Simulation | 2026-07-27 09:31:32 | 70 | ||||||
|
NEST Simulator Resource Report Resource Website 100+ mentions |
NEST Simulator (RRID:SCR_002963) | NEST | software application, simulation software, software resource | Software tool as simulator for spiking neural network models that focuses on dynamics, size and structure of neural systems rather than on exact morphology of individual neurons. Used for any size spiking neurons networks including models of information processing, models of network activity dynamics, models of learning and plasticity. | simulation, neuron, spiking, neural network, model, neural system, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: MUlti SImulation Coordinator has parent organization: NEST Initiative |
DOI:10.1007/978-1-4614-7320-6_258-5 | Free, Available for download, Freely available | nif-0000-00162, biotools:nest | https://github.com/nest/nest-simulator, https://bio.tools/nest | SCR_002963 | Neural Simulation Tool, NEural Simulation Tool, nest, nest-simulator | 2026-07-27 09:31:37 | 175 | |||||
|
OpenWorm Resource Report Resource Website 10+ mentions |
OpenWorm (RRID:SCR_014650) | software application, simulation software, web application, software resource | 3D web browser that allows users to simulate and dissect virtual C. elegans. Users can explore the anatomy of a virtual, 3D worm by zooming in and out, rotating the model, and viewing the worm's different layers. NeuroML format and connector are used to enhance the simulation, and supporting programs and code are available for coders. | simulation, model, web application, web browser, c elegans, nematode, worm, roundworm, open source, 3d, dissect, anatomy, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: WormBase is hosted by: GitHub |
PMID:25404913 DOI:10.3389/fncom.2014.00137 |
Open source, Code is available on GitHub, Available on the App Store | SCR_014984, biotools:OpenWorm | https://bio.tools/OpenWorm | SCR_014650 | OpenWorm Browser, Open Worm | 2026-07-27 09:34:45 | 21 |
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
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