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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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ProCon - PROteomics CONversion Resource Report Resource Website 1+ mentions |
ProCon - PROteomics CONversion (RRID:SCR_016363) | ProCon | software application, data processing software, software resource | Java based conversion tool for conversion of data from Proteomics files or a LIMS (Laboratory Information Management System) database into standard formats. Used to support wet-lab scientists in creating proteomics data files ready for upload into the public repositories. | data, proteomics, conversion, file, laboratory, information, management, system, database, standard, format, , bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Ruhr University Bochum; North Rhine-Westphalia; Germany |
European Union Projects ProDac ; European Union Projects ProteomeXchange ; the German Federal Ministry of Education and Research BMBF |
PMID:26182917 | Free, Available for download, Freely available | biotools:procon | https://bio.tools/procon | SCR_016363 | PROteomics CONversion | 2026-08-06 09:28:48 | 1 | ||||
|
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 | 2026-08-06 09:28:59 | 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 | 2026-08-06 09:28:57 | 1 | ||||||
|
STRUCTURE Resource Report Resource Website 1000+ mentions |
STRUCTURE (RRID:SCR_017637) | software toolkit, software resource | Software package for using multi locus genotype data to investigate population structure. Used for inferring presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed. Can be applied to most of commonly used genetic markers, including SNPS, microsatellites, RFLPs and Amplified Fragment Length Polymorphisms. | Multi locus genotype data, investigate population structure, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: STRAT has parent organization: Stanford University; Stanford; California works with: Structure Harvester |
PMID:21564903 PMID:18784791 PMID:12930761 PMID:10835412 |
Free, Available for download, Freely available | SCR_021634, nlx_154662, biotools:structure, SCR_002151 | https://bio.tools/structure, http://pritch.bsd.uchicago.edu/structure.html, | SCR_017637 | structure, Structure | 2026-08-06 09:29:07 | 4017 | ||||||
|
Racon Resource Report Resource Website 100+ mentions |
Racon (RRID:SCR_017642) | software application, data processing software, software resource | Software tool as de novo genome assembly from long uncorrected reads. Used to correct raw contigs generated by rapid assembly methods which do not include consensus step. Supports data produced by Pacific Biosciences and Oxford Nanopore Technologies. | Assembly, de novo, long, uncorrected, read, raw, contig, consensus, step, data, sequence, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
Croatian Science Foundation ; Croatian Academy of Sciences and Arts ; A*STAR ; Singapore |
DOI:10.1101/068122 | Free, Available for download, Freely available | OMICS_25714, biotools:Racon, BioTools:Racon | https://bio.tools/Racon, https://sources.debian.org/src/racon/ | SCR_017642 | 2026-08-06 09:29:10 | 149 | ||||||
|
seq-annot Resource Report Resource Website 1+ mentions |
seq-annot (RRID:SCR_018731) | standalone software, software application, 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 | 2026-08-06 09:29:22 | 1 | ||||||||
|
TransDecoder Resource Report Resource Website 1000+ mentions |
TransDecoder (RRID:SCR_017647) | standalone software, software application, data processing software, software resource | Software tool to identify candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to genome using Tophat and Cufflinks.Starts from FASTA or GFF file. Can scan and retain open reading frames (ORFs) for homology to known proteins by using BlastP or Pfam search and incorporate results into obtained selection. Predictions can then be visualized by using genome browser such as IGV. | Identify, candidate, coding, region, transcript, sequence, de novo, RNAseq, assembly, alignment, genome, open, reading, frame, homology, protein, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
Free, Available for download, Freely available | biotools:transDecoder, OMICS_10852 | https://bio.tools/TransDecoder, https://sources.debian.org/src/transdecoder/, https://github.com/TransDecoder/TransDecoder/wiki | SCR_017647 | , Find Coding Regions Within Transcripts | 2026-08-06 09:29:07 | 1309 | |||||||
|
Recognition of Errors in Assemblies using Paired Reads Resource Report Resource Website 1+ mentions |
Recognition of Errors in Assemblies using Paired Reads (RRID:SCR_017625) | REAPR | software application, data processing software, software resource | Software tool to identify errors in genome assemblies without need for reference sequence. Can be used in any stage of assembly pipeline to automatically break incorrect scaffolds and flag other errors in assembly for manual inspection. Reports mis-assemblies and other warnings, and produces new broken assembly based on error calls. | Identify, error, genome, assembly, without, reference, sequence, incorrect, scaffold, error |
is listed by: Debian is listed by: OMICtools has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
European Union ; Wellcome Trust ; JSPS KAKENHI |
PMID:23710727 | Free, Available for download, Freely available | OMICS_04068 | https://sources.debian.org/src/reapr/ | SCR_017625 | 2026-08-06 09:29:07 | 2 | |||||
|
QuPath Resource Report Resource Website 1000+ mentions |
QuPath (RRID:SCR_018257) | image analysis software, software application, 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 | 2026-08-06 09:29:16 | 1590 | ||||||
|
GeSeq Resource Report Resource Website 100+ mentions |
GeSeq (RRID:SCR_017336) | software application, service resource, data processing software, software resource | Software tool for rapid and accurate annotation of organelle genomes, in particular chloroplast genomes. | rapid, accurate, annotation, organelle, genome, chloroplast, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
Human Frontier Science Program ; Max Planck Society ; German Science Foundation |
PMID:28486635 | Free, Freely available | biotools:geseq | https://bio.tools/geseq | SCR_017336 | 2026-08-06 09:29:03 | 375 | ||||||
|
FlowCal Resource Report Resource Website 1+ mentions |
FlowCal (RRID:SCR_018140) | software application, data processing software, software resource | Open source software tool for automatically converting flow cytometry data from arbitrary to calibrated units. Can be run using intuitive Microsoft Excel interface, or customizable Python scripts. Software accepts Flow Cytometry Standard (FCS) files as inputs and is compatible with different calibration particles, fluorescent probes, and cell types. Automatically gates data, calculates common statistics, and produces plots. | Converting flow cytometry data, arbitrary unit, calibrated unit, data gating, statistic, plot, data, bio.tools |
is listed by: Debian is listed by: bio.tools |
NSF EFRI 1137266; NSF MCB 1244135; Office of Naval Research MURI N000141310074; Office of Naval Research YIP N000141410487; NIAID R21 AI115014; Welch Foundation ; NSF Graduate Research Fellowship DGE 0940902; NDSEG Fellowship |
PMID:27110723 | Free, Available for download, Freely available | biotools:flowcal | https://bio.tools/flowcal | SCR_018140 | Python Flow Cytometry Calibration Library | 2026-08-06 09:29:17 | 5 | |||||
|
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 | 2026-08-06 09:29:16 | 3 | |||||||
|
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 | 2026-08-06 09:29:31 | 0 | |||||||
|
CTDopts Resource Report Resource Website |
CTDopts (RRID:SCR_023997) | source code, software resource | Software gives your command-line tools a CTD-compatible interface. Module for enabling tools with CTD reading/writing, argument parsing, validating and manipulating capabilities. | command-line tools, CTD-compatible interface, module for enabling tools, CTD reading/writing, argument parsing, validating and manipulating capabilities, | is listed by: Debian | Free, Available for download, Freely available | https://sources.debian.org/src/ctdopts/ | SCR_023997 | ctdopts | 2026-08-06 09:30:17 | 0 | ||||||||
|
Htscodecs Resource Report Resource Website |
Htscodecs (RRID:SCR_024034) | source code, software resource | Software repository implements the custom CRAM codecs used for "EXTERNAL" block types.Custom compression for CRAM custom algorithm written to compress the BAM file format for DNA sequencing data. | custom CRAM codecs, EXTERNAL" block types, custom compression for CRAM, compress the BAM file format, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/htscodecs/ | SCR_024034 | htscodecs | 2026-08-06 09:30:14 | 0 | ||||||||
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conda-package-handling Resource Report Resource Website |
conda-package-handling (RRID:SCR_023991) | source code, software resource | Software to create and extract conda packages of various formats. | Create and extract conda packages, various formats, conda packages, | is listed by: Debian | Free, Available for download, Freely available | https://sources.debian.org/src/conda-package-handling/, https://conda.github.io/conda-package-handling/ | SCR_023991 | 2026-08-06 09:30:14 | 0 | |||||||||
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ELPH Resource Report Resource Website |
ELPH (RRID:SCR_024011) | source code, software resource | Software tool as general purpose Gibbs sampler for finding motifs in set of DNA or protein sequences.Takes as input a set containing sequences, and searches through them for the most common motif, assuming that each sequence contains one copy of the motif. Used to find patterns such as ribosome binding sites (RBSs) and exon splicing enhancers (ESEs). | Gibbs sampler, finding motifs, DNA sequences, protein sequences, common motif search, find patterns, ribosome binding sites, exon splicing enhancers, | is listed by: Debian | Free, Available for download, Freely available | OMICS_24617 | https://sources.debian.org/src/elph/ | SCR_024011 | Estimated Locations of Pattern Hits, elph | 2026-08-06 09:30:14 | 0 | |||||||
|
alleleCount Resource Report Resource Website 10+ mentions |
alleleCount (RRID:SCR_023961) | source code, software resource | Software package to prevent code duplication. Support code for NGS copy number algorithms. Generates count of coverage of each allele ACGT at that location given any filter settings. | NGS copy number, allele ACGT coverage, | is listed by: Debian | Free, Available for download, Freely available | https://sources.debian.org/src/allelecount/, http://cancerit.github.io/alleleCount/ | SCR_023961 | allelecount | 2026-08-06 09:30:13 | 12 | ||||||||
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Fast5 Library Resource Report Resource Website |
Fast5 Library (RRID:SCR_024023) | source code, software resource | Software C++ library for accessing Oxford Nanopore Technologies sequencing data. | C++ library, accessing Oxford Nanopore Technologies sequencing data, | is listed by: Debian | Free, Available for download, Freely available | OMICS_29589 | https://sources.debian.org/src/fast5/ | SCR_024023 | Fast5, fast5 | 2026-08-06 09:30:14 | 0 | |||||||
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python-biom-format Resource Report Resource Website 1+ mentions |
python-biom-format (RRID:SCR_024193) | source code, software resource | Software provides command line interface and Python API for working with Biological Observation Matrix files. | command line interface, Python API for working with Biological Observation Matrix files, BIOM files, |
is listed by: Debian is related to: biomformat |
PMID:23587224 | Free, Available for download, Freely available, | https://sources.debian.org/src/python3-biom-format/ | SCR_024193 | 2026-08-06 09:30:20 | 1 |
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