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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
NanoFilt Resource Report Resource Website 100+ mentions |
NanoFilt (RRID:SCR_016966) | software application, data processing software, software resource | Software tool written in Python to perform its filtering based on mean read quality and GC content and read length. Used for filtering and trimming of long read sequencing data. | filtering, trimming, long, sequencing, data, read |
is listed by: OMICtools is listed by: Debian |
Free, Available for download, Freely available | https://sources.debian.org/src/nanofilt/ | SCR_016966 | 2026-02-15 09:21:52 | 268 | |||||||||
|
ScaffMatch Resource Report Resource Website 1+ mentions |
ScaffMatch (RRID:SCR_017025) | software application, data processing software, software resource | Software tool as scaffolding algorithm based on maximum weight matching able to produce high quality scaffolds from next generation sequencing data (reads and contigs). Able to handle reads with both short and long insert sizes. | scaffolding, algorithm, maximum, weight, matching, next, generation, sequencing, data, read, contig, bio.tools |
uses: Python Programming Language is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Georgia State University; Georgia; USA |
NSF IIS 0916401 | PMID:25890305 | Free, Available for download, Freely available | biotools:scaffmatch, OMICS_08198 | http://alan.cs.gsu.edu/NGS/?q=content/scaffmatch https://bio.tools/scaffmatch |
SCR_017025 | 2026-02-15 09:21:54 | 1 | ||||||
|
halSynteny Resource Report Resource Website 1+ mentions |
halSynteny (RRID:SCR_018127) | software application, data processing software, software resource | Software tool as conserved synteny block construction method for multiple whole-genome alignments. Implementation of DAG-based for reconstruction of synteny blocks from genome alignment. | Conserved synteny, block construction method, genome alignment, DAG based reconstruction, synteny block, chromosome, bio.tools |
is listed by: Debian is listed by: bio.tools |
Free, Freely available | biotools:halSynteny | https://bio.tools/halSynteny | SCR_018127 | Hierarchical Alignment Format Synteny | 2026-02-15 09:22:18 | 3 | |||||||
|
seq-annot Resource Report Resource Website 1+ mentions |
seq-annot (RRID:SCR_018731) | software application, standalone software, software toolkit, software resource | Software Python package for annotating and counting genomic features in genomes and metagenomes. Software tools to facilitate annotation and comparison of genomes and metagenomes. | Annotating, counting, comparison, genomic feature, genome, metagenome, metagenomics, bio.tools |
is listed by: Debian is listed by: bio.tools |
Free, Available for download, Freely available | biotools:seq-annot | https://bio.tools/seq-annot | SCR_018731 | 2026-02-15 09:22:17 | 1 | ||||||||
|
CiLiQuant Resource Report Resource Website |
CiLiQuant (RRID:SCR_019319) | software application, data processing software, software resource | Software tool to separate junction reads based on their linear or circular origin. Only non ambiguous junction reads are used to compare relative linear and circular transcript abundance. | RNA, splicing, circular origin, separate junction reads, circular transcript abundance, linear transcript abundance, compare, bio.tools |
is listed by: bio.tools is listed by: Debian |
FWO ; Special Research Fund UGent ; Stichting Tegen Kanker ; Kom Op Tegen Kanker (Stand Up To Cancer) ; European Union's Horizon 2020 |
Free, Available for download, Freely available | biotools:ciliquant | https://bio.tools/ciliquant | SCR_019319 | 2026-02-15 09:21:53 | 0 | |||||||
|
QuPath Resource Report Resource Website 1000+ mentions |
QuPath (RRID:SCR_018257) | software application, image analysis software, data processing software, software resource | Open Source software package for digital pathology image analysis. Used for whole slide image analysis and digital pathology. Provides researchers with batch processing and scripting functionality, and extensible platform with which to develop and share new algorithms to analyze complex tissue images. | Digital pathology, image analysis, whole slide image, batch processing, tissue image, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Queens University Belfast; Ireland; United Kingdom |
Invest Northern Ireland ; Experimental Cancer Medicine Centre Network ; Sean Crummey Memorial Fund ; Tom Simms Memorial Fund ; Friends of the Cancer Centre ; Cancer Research UK Accelerator |
PMID:29203879 | Free, Available for download, Freely available | biotools:qupath | https://bio.tools/qupath | SCR_018257 | 2026-02-15 09:22:12 | 1590 | ||||||
|
Bio-EUtilities Resource Report Resource Website |
Bio-EUtilities (RRID:SCR_024064) | software toolkit, software resource | Software package which interacts with and retrieves data from NCBI's eUtils. This distribution encompasses low-level API for interacting with (and storing) information from NCBI's eUtils interface. See Bio::DB::EUtilities for the query API to retrieve data from NCBI, and Bio::Tools::EUtilities for the general class storage system. Note this may change to utilize the XML schema for each class at some point, though we will attempt to retain current functionality for backward compatibility unless this becomes problematic. | interacting, storing information, NCBI's eUtils interface, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/libbio-eutilities-perl/ | SCR_024064 | Bio-EUtilities - BioPerl low-level API for retrieving and storing data from NCBI eUtils, libbio-eutilities-perl | 2026-02-15 09:22:35 | 0 | ||||||||
|
Bio-Tools-Run-Alignment-Clustalw Resource Report Resource Website |
Bio-Tools-Run-Alignment-Clustalw (RRID:SCR_024067) | software toolkit, software resource | Software package for performing multiple sequence alignment from set of unaligned sequences and/or sub-alignments by means of the clustalw program. | performing multiple sequence alignment, set of unaligned sequences, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/libbio-tools-run-alignment-clustalw-perl/ | SCR_024067 | libbio-tools-run-alignment-clustalw-perl, Bio-Tools-Run-Alignment-Clustalw - Object for the calculation of a multiple sequence alignment from a set of unaligned sequences or alignments using the Clustalw program | 2026-02-15 09:23:32 | 0 | ||||||||
|
Tab2MAGE Resource Report Resource Website |
Tab2MAGE (RRID:SCR_024101) | software library, software toolkit, software resource | Software package written and supported by the ArrayExpress curation team, which aims to ease the process of submitting large microarray experiment datasets.Tab2MAGE uses flexible spreadsheet format for MIAME annotation of microarray experiments.Spreadsheets may be submitted directly to ArrayExpress, or used to generate MAGE-ML for data exchange. | ArrayExpress, submitting large microarray experiment datasets, spreadsheet format for MIAME annotation of microarray experiments, | is listed by: Debian | Free, Available for download, Freely available, | https://tab2mage.sourceforge.net/ | https://sources.debian.org/src/mage2tab/ | SCR_024101 | mage2tab, ArrayExpress Tab2MAGE | 2026-02-15 09:23:22 | 0 | |||||||
|
Bio-Tools-Phylo-PAML Resource Report Resource Website |
Bio-Tools-Phylo-PAML (RRID:SCR_024069) | software toolkit, software resource | Software package used to parse output from the PAML programs codeml, baseml, basemlg, codemlsites and yn00. You can use the Bio-Tools-Run-Phylo-PAML modules to actually run some of the PAML programs, but this module is only useful to parse the output. | parse output, PAML programs, codeml, baseml, basemlg, codemlsites, yn00. | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/libbio-tools-phylo-paml-perl/ | SCR_024069 | libbio-tools-phylo-paml-perl, Bio-Tools-Phylo-PAML - Parses output from the PAML programs codeml, baseml, codemlsites and yn00, basemlg | 2026-02-15 09:23:22 | 0 | ||||||||
|
Mapsembler2 Resource Report Resource Website 1+ mentions |
Mapsembler2 (RRID:SCR_024102) | software library, software toolkit, software resource | Targeted assembly software. It takes as input any number of NGS raw read sets and starter set of input sequences.May be used to Validate assembled sequence, Check if known enzyme is present in metagenomic NGS read set, Enrich unmappable reads by extending them, Check what happens at the extremities of a contig, Check the presence / absence and quantify RNA seq splicing events, Check presence/absence of SNPs or structural variants. | Targeted assembly, NGS raw read, input sequences, | is listed by: Debian | PMID:22443449 | Free, Available for download, Freely available, | OMICS_18310 | https://sources.debian.org/src/mapsembler2/ | SCR_024102 | mapsembler2, Mapsembler | 2026-02-15 09:23:20 | 1 | ||||||
|
MAXFLOW Resource Report Resource Website |
MAXFLOW (RRID:SCR_024103) | software library, software toolkit, software resource | Software library that implements the maxflow-mincut algorithm.Used for computing mincut/maxflow in a graph. | computing mincut/maxflow in a graph, | is listed by: Debian | DOI:10.1109/TPAMI.2004.60 | Free, Available for download, Freely available, | https://sources.debian.org/src/maxflow/ | SCR_024103 | maxflow | 2026-02-15 09:23:33 | 0 | |||||||
|
Bio-Graphics Resource Report Resource Website |
Bio-Graphics (RRID:SCR_024061) | software toolkit, software resource | Software package to generate GD images of Bio::Seq objects. | generate GD images of Bio::Seq objects, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/libbio-graphics-perl/ | SCR_024061 | Bio-Graphics - Generate GD images of Bio-Seq objects, libbio-graphics-perl | 2026-02-15 09:23:21 | 0 | ||||||||
|
CLI for BioMAJ Resource Report Resource Website |
CLI for BioMAJ (RRID:SCR_023980) | software toolkit, software resource | Software package to use BioMAJ providing biomaj-cli. | is listed by: Debian | Free, Available for download, Freely available | https://sources.debian.org/src/biomaj3-cli/ | SCR_023980 | biomaj3-cli, biomaj-cli | 2026-02-15 09:23:16 | 0 | |||||||||
|
BCALM 2 Resource Report Resource Website 1+ mentions |
BCALM 2 (RRID:SCR_023975) | software application, source code, software resource | Software tool for constructing compacted de Bruijn graph from sequencing data.Parallel algorithm that distributes the input based on minimizer hashing technique, allowing for good balance of memory usage throughout its execution. | constructing compacted de Bruijn graph, sequencing data, | is listed by: Debian | PMID:27307618 | Free, Available for download, Freely available | OMICS_12164 | https://sources.debian.org/src/bcalm/ | SCR_023975 | bcalm | 2026-02-15 09:23:19 | 3 | ||||||
|
GCLib Resource Report Resource Website |
GCLib (RRID:SCR_024028) | software library, software toolkit, software resource | Software genomic C++ library of reusable code for bioinformatics projects.Provides core collection of data structures, trying to avoid unnecessary code dependencies of other heavy libraries, while minimizing build time. | reusable code for bioinformatics, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/gclib/ | SCR_024028 | gclib, genome-code-lib | 2026-02-15 09:23:20 | 0 | ||||||||
|
CAT and BAT Resource Report Resource Website 1+ mentions |
CAT and BAT (RRID:SCR_023988) | software toolkit, software resource | Software pipeline for taxonomic classification of contigs and metagenome-assembled genomes. Contig Annotation Tool and Bin Annotation Tool for the taxonomic classification of long DNA sequences and metagenome assembled genomes of both known and unknown microorganisms, as generated by contemporary metagenomics studies. | taxonomic classification, long DNA sequences, metagenome assembled genomes, known and unknown microorganisms, contemporary metagenomics studies, | is listed by: Debian | PMID:31640809 | Free, Available for download, Freely available | https://sources.debian.org/src/cat-bat/ | SCR_023988 | Bin Annotation Tool, Contig Annotation Tool, BAT, CAT, cat-bat, CAT/BAT | 2026-02-15 09:22:34 | 2 | |||||||
|
limereg Resource Report Resource Website |
limereg (RRID:SCR_024097) | software library, software toolkit, software resource | Open source commandline based application and/or software development library, that performs 2D, rigid image registration on two greyscale images and outputs either the transformation parameters or the registered image. | 2D, rigid image registration, greyscale images, transformation parameters, registered image, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/limereg/ | SCR_024097 | 2026-02-15 09:23:22 | 0 | |||||||||
|
Libxdf Resource Report Resource Website |
Libxdf (RRID:SCR_024096) | software library, software toolkit, software resource | Software cross-platform C++ library for loading multimodal, multi-rate signals stored in XDF files. Used in biosignal viewing application SigViewer and the LSL application XDFStreamer. Can also be integrated into other C++ applications. | C++ library, loading multimodal, multi-rate signals, SigViewer, XDFStreamer, biosignal viewing, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/libxdf/ https://xdf-modules.github.io/libxdf/ |
SCR_024096 | libxdf, Libxdf � a C++ library for loading XDF files | 2026-02-15 09:22:36 | 0 | ||||||||
|
CTDConverter Resource Report Resource Website |
CTDConverter (RRID:SCR_024007) | software library, software toolkit, software resource | Software Python scripts to convert CTD files into other formats such as Galaxy, CWL. | Python, scripts to convert CTD files, Galaxy format, CWL format | is listed by: Debian | Free, Available for download, Freely available | https://sources.debian.org/src/ctdconverter/ | SCR_024007 | ctdconverter | 2026-02-15 09:22:34 | 0 |
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