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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Pilon Resource Report Resource Website 1000+ mentions |
Pilon (RRID:SCR_014731) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software tool to automatically improve draft assemblies and find variation among strains, including large event detection. FASTA files of genome along with one or more BAM files of reads aligned as input. Read alignment analysis is used to identify inconsistencies between input genome and evidence in reads, then attempts to make improvements to genome. | automatically, improve, draft, assembly, variation, strain, genome, read, alignment, analysis, inconsistency, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools is related to: shovill is hosted by: GitHub |
DOI:10.1371/journal.pone.0112963 DOI:10.1371/journal.pone.0112963 |
Available for download, Acknowledgement requested | OMICS_14553, biotools:pilon | https://github.com/broadinstitute/pilon/wiki, https://bio.tools/pilon, https://sources.debian.org/src/pilon/ | SCR_014731 | SciCrunch Registry | 2026-10-31 12:18:30 | 3377 | |||||||
|
Roary Resource Report Resource Website 500+ mentions |
Roary (RRID:SCR_018172) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software tool for rapid large scale prokaryote pan genome analysis. Builds large scale pan genomes, identifying core and accessory genes. Makes construction of pan genome of thousands of prokaryote samples on standard desktop without compromising on accuracy of results. Not intended for meta genomics or for comparing extremely diverse sets of genomes. | Genome analysis, prokaryote pan genome, pan genome, gene identification, analysis, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools works with: Scoary |
Wellcome Trust | PMID:26198102 | Free, Available for download, Freely available | OMICS_09491, biotools:roary | https://github.com/sanger-pathogens/Roary, https://bio.tools/roary, https://sources.debian.org/src/roary/ | SCR_018172 | SciCrunch Registry | 2026-10-31 12:18:43 | 710 | ||||||
|
StringTie Resource Report Resource Website 1000+ mentions |
StringTie (RRID:SCR_016323) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software application for assembling of RNA-Seq alignments into potential transcripts. It enables improved reconstruction of a transcriptome from RNA-seq reads. This transcript assembling and quantification program is implemented in C++ . | assembling, RNA, sequence, transcript, gene, alignment, reconstruction, read, analysis, process, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools |
NCI R01 CA120185; NCI R01 CA134292; NHGRI R01 HG006102; NHGRI R01 HG006677; NIGMS R01 GM105705; the Cancer Prevention and Research Institute of Texas |
PMID:25690850 DOI:10.1038/nbt.3122 |
Open source, Free, Freely available, Available for download | biotools:stringtie, OMICS_07226 | https://github.com/gpertea/stringtie, https://bio.tools/stringtie, https://sources.debian.org/src/stringtie/ | SCR_016323 | SciCrunch Registry | 2026-10-31 12:18:32 | 4976 | ||||||
|
fastp Resource Report Resource Website 1000+ mentions |
fastp (RRID:SCR_016962) | data analysis software, data processing software, software application, software resource | Software tool to provide fast all in one preprocessing for FastQ files. Developed in C++ with multithreading supported to afford high performance. Performs quality control, adapter trimming, quality filtering, per read quality pruning and many other operations with a single scan of the FASTQ data. | fast, all in one, preprocessing, FastQ, file, data, read, quality, control, adapter, trimming, filtering | is listed by: OMICtools | National Science Foundation of China ; Special Funds for Future Industries of Shenzhen |
PMID:30423086 | Free, Available for download, Freely available | SCR_016962 | SciCrunch Registry | 2026-10-31 12:18:34 | 1745 | ||||||||
|
Hinge Resource Report Resource Website 1+ mentions |
Hinge (RRID:SCR_016135) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software application for long read genome assembly based on hinging. Used in long-read sequencing technologies in genome assemblies to achieve optimal repeat resolution. | long, read, genome, assembly, hinging, sequence, optimal, repeat, resolution |
is listed by: Debian is listed by: OMICtools |
PMID:28320918 | Free, Available for download | OMICS_12339 | https://sources.debian.org/src/hinge/ | SCR_016135 | SciCrunch Registry | 2026-10-31 12:18:32 | 9 | |||||||
|
pheatmap Resource Report Resource Website 1000+ mentions |
pheatmap (RRID:SCR_016418) | pheatmap | data acquisition software, data processing software, image acquisition software, software application, software resource, software toolkit | Software tool as a function in R to draw clustered heatmaps for better control over graphical parameters. | draw, clustered, heatmap, control, graphical, parameter, size, shape, text, bio.tools |
is used by: ClustVis is listed by: Debian is listed by: bio.tools is listed by: OMICtools is listed by: SoftCite is related to: CRAN |
Free, Available for download, Freely available | biotools:pheatmap, OMICS_26726 | https://github.com/raivokolde/pheatmap, https://cran.r-project.org/web/packages/pheatmap/pheatmap.pdf, https://bio.tools/pheatmap, https://sources.debian.org/src/r-cran-pheatmap/ | SCR_016418 | SciCrunch Registry | pretty heatmap | 2026-10-31 12:18:42 | 1249 | ||||||
|
duphold Resource Report Resource Website 1+ mentions |
duphold (RRID:SCR_016938) | data analysis software, data processing software, software application, software resource | Software tool to annotate structural variant calls with sequence depth information that can add or remove confidence to SV predicted to affect copy number. Indicates the presence of a rapid change in depth relative to the regions surrounding the breakpoints. Allows the run time to be nearly independent of the number of variants important for large, jointly called projects with many samples. Annotates structural variant predictions made from both short read and long read data. | annotate, structural, variation, call, sequence, depth, confidence, predict, copy, number, short, long, read, data | is listed by: OMICtools | Free, Available for download, Freely available | SCR_016938 | SciCrunch Registry | 2026-10-31 12:18:33 | 3 | ||||||||||
|
FreeContact Resource Report Resource Website 10+ mentions |
FreeContact (RRID:SCR_016113) | alignment software, data processing software, image analysis software, software application, software resource | Alignment software for large-scale protein contact or protein-protein interaction prediction optimized for speed through shorter runtimes. FreeContact provides the opportunity to compute contact predictions in any environment (desktop or cloud). | protein, structure, prediction, sequence, analysis, fast, contact, alignment, multiple |
is listed by: OMICtools is related to: Debian |
Alexander von Humboldt Foundation ; German Ministry for Research and Education (BMBF: Bundesministerium fuer Bildung und Forschung) ; Research Council of Norway 208481 |
PMID:24669753 DOI:10.1186/1471-2105-15-85 |
Open source, Free, Available for download | OMICS_03520 | https://rostlab.org/owiki/index.php/FreeContact, https://sources.debian.org/src/libfreecontact-perl/ | SCR_016113 | SciCrunch Registry | 2026-10-31 12:18:42 | 22 | ||||||
|
ClonalOrigin Resource Report Resource Website 1+ mentions |
ClonalOrigin (RRID:SCR_016061) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software package for comparative analysis of the sequences of a sample of bacterial genomes in order to reconstruct the recombination events that have taken place in their ancestry. | comparative, analysis, sequence, bacteria, genome, reconstruct, recombination, events, ancestry, bayesian |
is listed by: Debian is listed by: OMICtools is related to: Imperial College London; London; United Kingdom is related to: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
National Science Foundation DBI-0630765; Science Foundation of Ireland 05/FE1/B882; Wellcome Trust WT082930MA |
PMID:20923983 DOI:10.1534/genetics.110.120121 |
Free, Available for download | OMICS_18881 | https://sources.debian.org/src/clonalorigin/ | SCR_016061 | SciCrunch Registry | 2026-10-31 12:18:33 | 8 | ||||||
|
mlgt Resource Report Resource Website |
mlgt (RRID:SCR_001211) | mlgt | data processing software, software application, software resource | Software for processing and analysis of high throughput (Roche 454) sequences generated from multiple loci and multiple biological samples. Sequences are assigned to their locus and sample of origin, aligned and trimmed. Where possible, genotypes are called and variants mapped to known alleles. | roche, windows, os x, genotype, variant, allele, high throughput sequencing, locus, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University of Manchester; Manchester; United Kingdom |
THIS RESOURCE IS NO LONGER IN SERVICE | BioTools:mlgt, OMICS_02131, biotools:mlgt | https://bio.tools/mlgt, https://bio.tools/mlgt, https://bio.tools/mlgt | SCR_001211 | SciCrunch Registry | Multi-Locus Geno-Typing, mlgt: Multi-Locus Geno-Typing | 2026-10-31 12:19:05 | 0 | ||||||
|
RDPipeline Resource Report Resource Website 10+ mentions |
RDPipeline (RRID:SCR_001192) | RDPipeline | data processing software, software application, software resource | Software to simplify the processing of large rRNA sequence libraries (including single-strand and paired-end reads) obtained through high-throughput sequencing technology. Tools for assembly, quality filtering, taxonomy based analysis and taxonomy independent analysis tools, and tools to convert the data to formats suitable for common ecological and statistical packages are available. For extremely large datasets, command line tools are available. | amplicon sequencing, high-throughput sequencing, rrna, assembly, quality filtering, taxonomy, analysis, FASEB list |
is listed by: OMICtools has parent organization: Ribosomal Database Project |
PMID:24288368 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02158 | SCR_001192 | SciCrunch Registry | RDP Pipeline, RDP Amplicon Sequence Pipeline | 2026-10-31 12:19:05 | 39 | ||||||
|
Plantagora Resource Report Resource Website 1+ mentions |
Plantagora (RRID:SCR_001227) | Plantagora | data or information resource, data set, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 18,2025. A web-based plant genome assembly simulation platform whose resources include out of the box scripts for analyzing assembly data, an on-demand web graphing tool to model your experiment, and a downloadable database with metrics and parameters from over 3,000 simulated genome assemblies. | next-generation sequencing, genome assembly, sequencing, genome, 454, illumina, simulate |
is listed by: OMICtools has parent organization: University of Arizona; Arizona; USA |
PMID:22174807 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02116 | SCR_001227 | SciCrunch Registry | Plantagora - a resource for plant genome assembly | 2026-10-31 12:19:05 | 1 | ||||||
|
Avadis Resource Report Resource Website 1+ mentions Rating or validation data |
Avadis (RRID:SCR_000644) | Avadis | software library, software resource, software toolkit | Software integrated platform that provides analysis, management and visualization tools for next-generation sequencing data. It supports workflows for RNA-Seq, DNA-Seq, ChIP-Seq and small RNA-Seq experiments. Avadis has a built-in Gene Ontology browser to view ontology hierarchies. There are common ontology paths for multiple genes. Platform has collection of data / text mining algorithms, data visualization libraries, workflow/application automation layers, and enterprise data organization functions. These functions are available as libraries that allow developers to rapidly build software prototypes, applications and off-the-shelf products. The collection of algorithms and visualizations in AVADIS grows as new applications using the platform are developed. Currently, the algorithms that AVADIS platform contains range from general purpose statistical mining and modelling algorithms, to text mining algorithms, to very application-specific algorithms for microarray / NGS data analysis, QSAR modelling and biological networks analysis. AVADIS has a collection of powerful mining algorithms like PCA, ANOVA, T-test, clustering, classification and regression methods. The range of visualizations includes most statistical and data modelling related graphing views, and very application-specific visualizations. Some of the statistical views include 2D/3D scatter plots, profile plots, heat maps, histograms and matrix plot; data modelling relevant views include dendrograms, cluster profiles, similarity images and SOM U-matrices. Application-specific views in AVADIS include pathway network views, genome browsers, chemical structure views and pipe-line views. Platform: Windows compatible, Mac OS X compatible, Linux compatible, | pathway network views, genome browsers, chemical structure views, pipe-line views, next-generation sequencing data, integrated platform, view ontology hierarchies, statistical mining and modelling, collection of data, text mining algorithms collection, data visualization libraries, |
is listed by: Gene Ontology Tools is listed by: OMICtools is related to: Gene Ontology |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01120, nlx_149208 | http://www.strandls.com/Avadis | SCR_000644 | SciCrunch Registry | Access Visualize Analyze Discover, Avadis NGS | 2026-10-31 12:19:04 | 2 | ||||||
|
MaryGold Resource Report Resource Website 1+ mentions |
MaryGold (RRID:SCR_000528) | MaryGold | software resource, software toolkit | Software package that enables detection of sequence variation between metagenomic samples. | sequence variation, metagenomic, c++, python |
is listed by: OMICtools has parent organization: SourceForge |
Free, Available for download, Freely available, | OMICS_01495 | SCR_000528 | SciCrunch Registry | MaryGold - Variation analysis of metagenomic samples | 2026-10-31 12:19:06 | 1 | |||||||
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MAIA (Microarray Image Analysis) Resource Report Resource Website 1+ mentions |
MAIA (Microarray Image Analysis) (RRID:SCR_002239) | MAIA | data processing software, image analysis software, software application, software resource | Software package for automatic processing of the one- and two- (typically, Cy3-green/Cy5-red) color images produced in cDNA, CGH (comparative genome hybridization) or protein microarray technologies. It incorporates the following modules: * The spot localization module (i) identifies the position of each spot on the array, so that the name of the spotted clone can be associated with the correspondent spot; and (ii) establishes the borders between the neighborhood spots letting one to perform further data processing procedures (i.e. to extract quantitative information) for each spot independently of the other neighborhood spots. Visually this results in the generation of a grid covering the image. The spot localization algorithm is fully automatic and robust with respect to deviations from perfect spot alignment and contamination. As an input, it requires only the common array design parameters: number of blocks and number of spots in the x and y directions of the array. * The spot quantification module for one-color images performs segmentation of the spots and estimates the averaged spot and local background intensities. The spot quantification module for two-color images estimates the ratio of the measured intensities in the two color channels at each spot reflecting differential gene (cDNA technology) or protein expression or a change in DNA copy number (CGH experiments) between the test and control samples for the corresponding gene. This module includes algorithms based on the linear regression and segmentation of the spots. A special procedure for detection and removal of the aberrant pixels has been developed to make ratio estimates more resistant to array contamination. It ensures more consistent ratio estimates obtained from different algorithms, and allows delivery of a single trustable ratio value. * The quality control module provides a value of spot quality reflecting the level of confidence in the obtained quantitative estimates at each spot. These quality values can be used either directly to flag out some spots with the quality lower than the user-defined threshold, or in the follow-up analysis as a weight controlling the contribution/influence of the obtained ratio estimates. The unique spot quality value for a spot is derived from a set of marginal quality parameters characterizing certain features of the spot. The contribution of each quality parameter in the overall quality is automatically evaluated based on the user visual classification of the spots, or using information available from the replicated spots, located at the same array or over a set of replicated arrays. * The image simulator allows the generation of a broad spectrum of microarray images with different types of contamination (like non-specific hybridization and dust) and noise. Since in simulation experiment the true values of the ratios are known exactly, it allows one to evaluate, to test and to compare different algorithms for microarray image processing objectively. | microarray, cdna, comparative genome hybridization, protein microarray |
is listed by: OMICtools has parent organization: Curie Institute; Paris; France |
PMID:17237062 PMID:16374914 |
Free, Available for download, Freely available | OMICS_00843 | SCR_002239 | SciCrunch Registry | Microarray Image Analysis | 2026-10-31 12:19:06 | 3 | ||||||
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biobambam Resource Report Resource Website 50+ mentions |
biobambam (RRID:SCR_003308) | data processing software, software application, software resource | Software tools for read pair collation based algorithms on BAM files including * bamcollate2: reads BAM and writes BAM reordered such that alignment or collated by query name * bammarkduplicates: reads BAM and writes BAM with duplicate alignments marked using the BAM flags field * bammaskflags: reads BAM and writes BAM while masking (removing) bits from the flags column * bamrecompress: reads BAM and writes BAM with a defined compression setting. This tool is capable of multi-threading. * bamsort: reads BAM and writes BAM resorted by coordinates or query name * bamtofastq: reads BAM and writes FastQ; output can be collated or uncollated by query name | standalone software, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
DOI:10.1186/1751-0473-9-13 | Free, Available for download, Freely available | biotools:biobambam, OMICS_04664 | https://bio.tools/biobambam, https://sources.debian.org/src/biobambam2/ | SCR_003308 | SciCrunch Registry | 2026-10-31 12:19:08 | 65 | |||||||
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FASTX-Toolkit Resource Report Resource Website 1000+ mentions |
FASTX-Toolkit (RRID:SCR_005534) | data processing software, software application, software resource, software toolkit | Software tool as collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing. | Short reads, FASTA file, FASTQ file, preprocessing, command line tools, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Cold Spring Harbor Laboratory |
SCR_019035, SCR_015042, biotools:fastx-toolkit, OMICS_01045 | https://github.com/agordon/fastx_toolkit, https://bio.tools/fastx-toolkit | SCR_005534 | SciCrunch Registry | FASTQ/A short-reads pre-processing tools | 2026-10-31 12:19:10 | 2864 | ||||||||
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Sickle Resource Report Resource Website 1000+ mentions |
Sickle (RRID:SCR_006800) | Sickle | data processing software, software application, software resource | Software tool for windowed adaptive trimming for fastq files using quality. Supports quality values like Illumina, Solexa, and Sanger. Takes the quality values and slides a window across them whose length is 0.1 times the length of the read. | bio.tools, windowed, adaptive, trimming, FASTQ, quality, value, read |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
Free, Available for download, Freely available | OMICS_01077, biotools:sickle, SCR_016901 | https://bio.tools/sickle, https://sources.debian.org/src/sickle/ | SCR_006800 | SciCrunch Registry | sickle - A windowed adaptive trimming tool for FASTQ files using quality | 2026-10-31 12:19:11 | 1664 | ||||||
|
STRAP Resource Report Resource Website 100+ mentions |
STRAP (RRID:SCR_005675) | STRAP | data processing software, software application, software resource | Software program that automatically annotates a protein list with information that helps in the meaningful interpretation of data from mass spectrometry and other techniques. It takes protein lists as input, in the form of plain text files, protXML files (usually from the TPP), or Dat files from MASCOT search results. From this, it generates protein annotation tables, and a variety of GO charts to aid individual and differential analysis of proteomics data. It downloads information from mainly the Uniprot and EBI QuickGO databases. STRAP requires Windows XP or higher with at least version 3.5 of the Microsoft .NET Framework installed. Platform: Windows compatible | protein, gene, annotation, mass spectrometry, proteomics, visualization, browser, differential analysis, analysis, ontology or annotation browser, ontology or annotation visualization, differential analysis of proteomics data sets, windows, protein annotation, data visualization, c#, pathway, FASEB list |
is listed by: Gene Ontology Tools is listed by: OMICtools is related to: Gene Ontology is related to: UniProt is related to: QuickGO has parent organization: Boston University School of Medicine; Massachusetts; USA |
NHLBI contract N01 HV28178; NCRR P41 RR10888 |
PMID:19839595 | Open unspecified license, Acknowledgement requested | OMICS_02277, nlx_149115 | SCR_005675 | SciCrunch Registry | Software Tool for Rapid Annotation of Proteins, STRAP for GO Annotation, STRAP - Software Tool for Rapid Annotation of Proteins | 2026-10-31 12:19:10 | 122 | |||||
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SOAP3 Resource Report Resource Website 1+ mentions |
SOAP3 (RRID:SCR_005502) | SOAP3 | data processing software, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 12,2024. GPU-based software for aligning short reads with a reference sequence. It can find all alignments with k mismatches, where k is chosen from 0 to 3. | gpu/cuda, next generation sequencing, alignment, short read, gpu |
is listed by: OMICtools has parent organization: SOAP |
PMID:22285832 | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_005502 | SciCrunch Registry | 2026-10-31 12:19:10 | 7 |
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