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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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OligoWiz Resource Report Resource Website 10+ mentions |
OligoWiz (RRID:SCR_012966) | OligoWiz | production service resource, software resource, data analysis service, analysis service resource, service resource | Software and server that performs intelligent design of oligonucleotides for DNA microarrays. |
is listed by: OMICtools has parent organization: DTU Center for Biological Sequence Analysis |
PMID:18007603 PMID:15980547 |
OMICS_00831 | SCR_012966 | 2026-08-08 12:02:37 | 10 | |||||||||
|
miRecords Resource Report Resource Website 100+ mentions |
miRecords (RRID:SCR_013021) | miRecords | data or information resource, database, service resource, storage service resource, data repository | A resource for animal miRNA-target interactions consisting of the Validated Targets component, a large, high-quality database of experimentally validated miRNA targets resulting from meticulous literature curation, and the Predicted Targets component, an integration of predicted miRNA targets produced by 11 established miRNA target prediction programs. April 27, 2013, the Validated Targets component of miRecords hosts 2705 records of interactions between 644 miRNAs and 1901 target genes in 9 animal species. Among these records, 2028 were curated from low throughput experiments. The Predicted Targets component of mIRecords integrates the predicted targets of the following miRNA target prediction tools: DIANA-microT, MicroInspector, miRanda, MirTarget2, miTarget, NBmiRTar, PicTar, PITA, RNA22, RNAhybrid, and TargetScan/TargertScanS. We would be glad to include your experimentally validated miRNA target data (published or unpublished) into miRecords., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | FASEB list | is listed by: OMICtools | PMID:18996891 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00405 | https://omictools.com/mirecords-tool | http://mirecords.umn.edu/miRecords/ | SCR_013021 | 2026-08-08 12:02:33 | 452 | |||||
|
Pilon Resource Report Resource Website 1000+ mentions |
Pilon (RRID:SCR_014731) | sequence analysis software, software resource, software application, data analysis software, data processing software | 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 | 2026-08-08 12:02:38 | 3377 | |||||||
|
StringTie Resource Report Resource Website 1000+ mentions |
StringTie (RRID:SCR_016323) | sequence analysis software, software resource, software application, data analysis software, data processing software | 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 |
the Cancer Prevention and Research Institute of Texas ; NHGRI R01 HG006677; NIGMS R01 GM105705; NHGRI R01 HG006102; NCI R01 CA120185; NCI R01 CA134292 |
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 | 2026-08-08 12:02:31 | 4976 | ||||||
|
fastp Resource Report Resource Website 1000+ mentions |
fastp (RRID:SCR_016962) | software resource, software application, data analysis software, data processing software | 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 | Special Funds for Future Industries of Shenzhen ; National Science Foundation of China |
PMID:30423086 | Free, Available for download, Freely available | SCR_016962 | 2026-08-08 12:02:40 | 1745 | ||||||||
|
Hinge Resource Report Resource Website 1+ mentions |
Hinge (RRID:SCR_016135) | sequence analysis software, software resource, software application, data analysis software, data processing software | 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 | 2026-08-08 12:02:31 | 9 | |||||||
|
pheatmap Resource Report Resource Website 1000+ mentions |
pheatmap (RRID:SCR_016418) | pheatmap | image acquisition software, software toolkit, data acquisition software, software resource, software application, data processing software | 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 | pretty heatmap | 2026-08-08 12:02:39 | 1249 | ||||||
|
duphold Resource Report Resource Website 1+ mentions |
duphold (RRID:SCR_016938) | software resource, software application, data analysis software, data processing software | 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 | 2026-08-08 12:02:36 | 3 | ||||||||||
|
FreeContact Resource Report Resource Website 10+ mentions |
FreeContact (RRID:SCR_016113) | image analysis software, software resource, software application, alignment software, data processing software | 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 | 2026-08-08 12:02:39 | 22 | ||||||
|
ClonalOrigin Resource Report Resource Website 1+ mentions |
ClonalOrigin (RRID:SCR_016061) | sequence analysis software, software resource, software application, data analysis software, data processing software | 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 |
Wellcome Trust WT082930MA; National Science Foundation DBI-0630765; Science Foundation of Ireland 05/FE1/B882 |
PMID:20923983 DOI:10.1534/genetics.110.120121 |
Free, Available for download | OMICS_18881 | https://sources.debian.org/src/clonalorigin/ | SCR_016061 | 2026-08-08 12:02:39 | 8 | ||||||
|
Roary Resource Report Resource Website 500+ mentions |
Roary (RRID:SCR_018172) | sequence analysis software, software resource, software application, data analysis software, data processing software | 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 | 2026-08-08 12:02:32 | 710 | ||||||
|
iontree Resource Report Resource Website |
iontree (RRID:SCR_002813) | software resource | Software package that provides utility functions to manage and analyse MS2/MS3 fragmentation data from ion trap mass spectrometry. It was designed for high throughput metabolomics data with many biological samples and a large numer of ion trees collected. Tests have been done with data from low-resolution mass spectrometry but could be readily extended to precursor ion based fragmentation data from high resoultion mass spectrometry. | standalone software, mac os x, unix/linux, windows, r, mass spectrometry, metabolomics, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
PMID:24958264 | Free, Freely available, Available for download | OMICS_02656, biotools:iontree | https://bio.tools/iontree | SCR_002813 | iontree: Data management and analysis of ion trees from ion-trap mass spectrometry | 2026-08-08 12:02:51 | 0 | ||||||
|
HPeak Resource Report Resource Website 1+ mentions |
HPeak (RRID:SCR_010859) | HPeak | software resource | A Hidden Markov Model-based algorithm for the purpose of defining genome-wide ChIP-enriched peaks in the human genome using short sequence reads. |
is listed by: OMICtools has parent organization: University of Michigan; Ann Arbor; USA |
OMICS_00444 | SCR_010859 | HPeak: An HMM-based algorithm for defining read-enriched regions from massive parallel sequencing data | 2026-08-08 12:02:41 | 1 | |||||||||
|
MochiView Resource Report Resource Website 1+ mentions |
MochiView (RRID:SCR_000259) | MochiView | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 30,2022. Java software that integrates browsing of genomic sequences, features, and data with DNA motif visualization and analysis. | java |
is listed by: OMICtools has parent organization: University of California at San Francisco; California; USA |
PMID:20409324 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02174 | SCR_000259 | 2026-08-08 12:02:39 | 3 | |||||||
|
SOAPsplice Resource Report Resource Website 1+ mentions |
SOAPsplice (RRID:SCR_013253) | SOAPsplice | software resource | A tool for genome-wide ab initio detection of splice junction sites from RNA-Seq, a method using new generation sequencing technologies to sequence the messenger RNA. | is listed by: OMICtools | PMID:22303342 | OMICS_01251 | SCR_013253 | 2026-08-08 12:02:41 | 7 | |||||||||
|
MUMmer Resource Report Resource Website 500+ mentions |
MUMmer (RRID:SCR_018171) | image analysis software, software resource, software application, alignment software, data processing software | Software package as system for rapidly aligning entire genomes. Alignment tool for DNA and protein sequences. Can align incomplete genomes. | Align, genome, DNA, protein, sequence, , bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools is listed by: SoftCite is related to: MUMmerGPU |
NLM R01 LM06845; NSF IIS 9902923; NIAID N01 AI15447 |
PMID:14759262 | Free, Available for download, Freely available | OMICS_14554, biotools:mummer | https://github.com/mummer4/mummer, https://bio.tools/mummer, https://sources.debian.org/src/mummer/ | SCR_018171 | MUMmer4, MUMmer 3.0 | 2026-08-08 12:01:14 | 547 | |||||
|
APHA Resource Report Resource Website 100+ mentions |
APHA (RRID:SCR_012000) | APHA | data or information resource, portal, organization portal | The oldest and most diverse organization of public health professionals in the world and has been working to improve public health since 1872. | is listed by: OMICtools | OMICS_01789 | SCR_012000 | American Public Health Association | 2026-08-08 12:03:11 | 231 | |||||||||
|
Argo Genome Browser Resource Report Resource Website 1+ mentions |
Argo Genome Browser (RRID:SCR_011763) | Argo Genome Browser | data or information resource, software resource, data set | A tool for visualizing and manually annotating whole genomes that can be run as Applet or Webstart application as well as standalone application. |
is listed by: OMICtools has parent organization: Broad Institute |
Open unspecified license, Free | OMICS_00902 | SCR_011763 | 2026-08-08 12:03:16 | 5 | |||||||||
|
Trimmomatic Resource Report Resource Website 10000+ mentions |
Trimmomatic (RRID:SCR_011848) | Trimmomatic | software resource, software application, 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 | 2026-08-08 12:03:16 | 23444 | |||||
|
BIDS Validator Resource Report Resource Website 10+ mentions |
BIDS Validator (RRID:SCR_017255) | software resource, software application, data processing software | Software validation tool that checks submitted folder structure for compliance to BIDS data standard. Validates Brain Imaging Data Structure. | BIDS, NeuroImaging, Neuroscience, check, folder, structure, compliance, data, standard, brain, imaging | is listed by: OMICtools | Laura and John Arnold Foundation ; NIBIB R01 EB020740 |
PMID:28278228 | Free, Available for download, Freely available | http://bids-standard.github.io/bids-validator/ | SCR_017255 | Brain Imaging Data Structure (BIDS) Validator | 2026-08-08 12:03:17 | 26 |
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