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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
xia2 pipeline Resource Report Resource Website 10+ mentions |
xia2 pipeline (RRID:SCR_015746) | software application, data processing software, software resource | 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 | 2026-08-06 09:28:43 | 34 | |||||||
|
rnaQUAST Resource Report Resource Website 1+ mentions |
rnaQUAST (RRID:SCR_016994) | software application, data processing software, software resource | 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 | 2026-08-06 09:28:59 | 3 | ||||||
|
Ffindex Resource Report Resource Website |
Ffindex (RRID:SCR_016110) | source code, database, data or information resource, software resource | Database and index for huge amounts of small files. Files are stored concatenated in one big data file, with second file contains plain text index, giving name, offset and length of small files. | simple, index, database, huge, amount, small file | is listed by: Debian | Free, Available for download, Freely available | https://sources.debian.org/src/ffindex/, https://github.com/ahcm/ffindex | SCR_016110 | 2026-08-06 09:28:45 | 0 | |||||||||
|
Oufti Resource Report Resource Website 10+ mentions |
Oufti (RRID:SCR_016244) | image analysis software, software application, data processing software, software resource | Software designed for analysis of microscopy data. It performs sub-pixel precision detection, quantification of cells and fluorescence signals, as well as other image analysis functions. | microscopy, data, imaging, image, analysis, pixel, fluorescent, bio.tools |
is listed by: Debian is listed by: bio.tools |
NIGMS R01 GM065835 | PMID:26538279 | biotools:oufti | https://bio.tools/oufti | SCR_016244 | outfi | 2026-08-06 09:28:49 | 13 | ||||||
|
Porechop Resource Report Resource Website 1000+ mentions |
Porechop (RRID:SCR_016967) | software application, data processing software, software resource | 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 | 2026-08-06 09:28:56 | 1100 | ||||||||
|
PASTEClassifier Resource Report Resource Website 10+ mentions |
PASTEClassifier (RRID:SCR_017645) | PASTEC | software application, data processing software, software resource | 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 | 2026-08-06 09:29:10 | 11 | ||||
|
Sniffles Resource Report Resource Website 50+ mentions |
Sniffles (RRID:SCR_017619) | software application, data processing software, software resource | 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 | 2026-08-06 09:29:07 | 59 | ||||||
|
MEGAHIT Resource Report Resource Website 1000+ mentions |
MEGAHIT (RRID:SCR_018551) | software application, data processing software, software resource | 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 | 2026-08-06 09:29:27 | 1451 | |||||
|
TGS-GapCloser Resource Report Resource Website 10+ mentions |
TGS-GapCloser (RRID:SCR_017633) | software application, data processing software, software resource | 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 | 2026-08-06 09:29:10 | 35 | ||||||||
|
parSMURF Resource Report Resource Website 1+ mentions |
parSMURF (RRID:SCR_017560) | software application, data processing software, software resource | 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 | 2026-08-06 09:29:06 | 1 | ||||||||
|
EHRtemporalVariability Resource Report Resource Website 1+ mentions |
EHRtemporalVariability (RRID:SCR_018663) | software application, data processing software, software resource | 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 | 2026-08-06 09:29:28 | 3 | ||||||
|
gffread Resource Report Resource Website 10+ mentions |
gffread (RRID:SCR_018965) | software application, data processing software, software resource | 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 | 2026-08-06 09:29:25 | 26 | ||||||
|
Pychopper Resource Report Resource Website 10+ mentions |
Pychopper (RRID:SCR_018966) | software application, data processing software, software resource | 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 | 2026-08-06 09:29:30 | 26 | ||||||||
|
rna-stability Resource Report Resource Website 1+ mentions |
rna-stability (RRID:SCR_019259) | software application, data processing software, software resource | 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 | 2026-08-06 09:29:27 | 1 | ||||||||
|
mosdepth Resource Report Resource Website 10+ mentions |
mosdepth (RRID:SCR_018929) | software application, data processing software, software resource | 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 | 2026-08-06 09:29:24 | 38 | ||||||
|
RADAR-base Resource Report Resource Website 1+ mentions |
RADAR-base (RRID:SCR_019233) | portal, project portal, data or information resource | Open source mobile health platform for collecting, monitoring, and analyzing data using sensors, wearables, and mobile devices. Enables study design and set up, active and passive remote data collection, secure data transmission via Wifi and/or Bluetooth and scalable solutions for data storage, management and access. Allows study participants to share their health data with clinicians and researchers in secure way. | Data collection, remote data collection, data collection platform, collecting mHealth datasets, mental health, mobile applications, remote sensing technology, telemedicine, bio.tools |
is listed by: bio.tools is listed by: Debian |
GSTT Charity ; Maudsley Charity ; NIHR Biomedical Research Centre at South London ; Maudsley NHS Foundation Trust ; King’s College London ; EU IMI2 ; UK National Institute for Health Research |
Free, Available for download, Freely available | biotools:RADAR-base | https://radar-base.org/index.php/getting-started-with-radar-base/, https://radar-base.org/index.php/getting-started-with-radar-base/demo-using-prmt-app/, https://bio.tools/RADAR-base | SCR_019233 | Remote Assessment of Disease And Relapses, Radar-base | 2026-08-06 09:29:32 | 1 | ||||||
|
Placnet Resource Report Resource Website |
Placnet (RRID:SCR_024176) | software library, software toolkit, software resource | Software Perl tools for plasmid analysis in NGS projects.Identifies, visualizes and analyzes plasmids in WGS projects by creating a network of contig interactions, thus allowing comprehensive plasmid analysis within WGS datasets.Optimized to work with Illumina sequences but it also works with 454, Iontorrent or any of the actual sequence technologies. The input of placnet is a set of contigs and one or more SAM files with the mapping of the reads against the contigs. Placnet obtains a set of files, easily opened on Cytoscape software or other network tools. | plasmid constellation networks, identifies splasmids, visualizes and analyzes plasmids, WGS projects, creating network of contig interactions, comprehensive plasmid analysis within WGS datasets, | is listed by: Debian | PMID:25522143 | Free, Available for download, Freely available, | OMICS_11487 | https://sources.debian.org/src/placnet/ | SCR_024176 | plasmid constellation networks, placnet | 2026-08-06 09:30:20 | 0 | ||||||
|
PRINSEQ Resource Report Resource Website 50+ mentions |
PRINSEQ (RRID:SCR_024178) | software library, software toolkit, software resource | Software Perl application for quality control and data preprocessing of genomic and metagenomic datasets. Used to filter, reformat, or trim genomic and metagenomic sequence data. Generates summary statistics of sequences in graphical and tabular format. | data quality control, data preprocessing, genomic and metagenomic datasets, | is listed by: Debian | PMID:21278185 | Free, Available for download, Freely available, | https://sources.debian.org/src/prinseq-lite/ | SCR_024178 | prinseq-lite | 2026-08-06 09:30:17 | 72 | |||||||
|
POA Resource Report Resource Website |
POA (RRID:SCR_024172) | software library, software toolkit, software resource | Software application for multiple sequence alignment in bioinformatics. Has superior ability to handle branching / indels in the alignment. | sequence alignment, multiple sequence alignment, handle branching in alignment, handle indels in alignment, | is listed by: Debian | DOI:10.1093/bioinformatics/bth126 | Free, Available for download, Freely available, | OMICS_14254 | https://sources.debian.org/src/poa/ | SCR_024172 | poa, Partial Order Alignment | 2026-08-06 09:30:20 | 0 | ||||||
|
PLIP Resource Report Resource Website 100+ mentions |
PLIP (RRID:SCR_024173) | software library, software toolkit, software resource | Software application as protein�ligand interaction profiler to identify non-covalent interactions between biological macromolecules and their ligands. Provides atom level information on binding characteristics as well as publication ready visualizations and parsable output files. PLIP web tool is based on PLIP command line tool and offers graphical interface for analysis of few structures. | Protein Ligand Interaction Profiler, | is listed by: Debian | DOI:10.1093/nar/gkv315 | Free, Available for download, Freely available, | OMICS_08028 | https://sources.debian.org/src/plip/, https://github.com/pharmai/plip | SCR_024173 | Protein-Ligand Interaction Profiler, plip | 2026-08-06 09:30:16 | 109 |
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