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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Clippers Resource Report Resource Website 1+ mentions |
Clippers (RRID:SCR_005256) | Clippers | software resource | A software program designed to identify long deletions of a genome as well as the RNA splicings using long Illumina reads. Currently, Clippers is implemented for long reads Illumina, ex: 75bp or 100bp, allowing mismatches and a single deletion/splicing. Clippers is a sister tool of PerM, our short reads aligner. Users are strongly suggested to use PerM to initially mapped reads and identify the deletion/splicing with the initially unmapped reads. We plan to extend it to ABI SOLiD reads in the near future. Clippers outputs gap-alignments in SAM format. You can use SAMtools or other program to interpret the deletion/splicing. The input files are a reference in fasta format and the reads is in fasta or fastq format. | long deletion, genome, rna splicing, illumina, deletion |
is listed by: OMICtools is related to: PerM has parent organization: Google Code has parent organization: University of Southern California; Los Angeles; USA |
PMID:19675096 | GNU General Public License, v2, Acknowledgement requested | OMICS_00311 | SCR_005256 | clippers - Deletion Identification Program using Periodic Spaced Seed | 2026-09-19 12:50:50 | 7 | ||||||
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Moa Resource Report Resource Website |
Moa (RRID:SCR_005373) | Moa | software resource | Software to assist a bioinformatician to organize, document, share, execute and repeat workflows in a command line environment without losing any of the flexibility of the command line, and, at all times giving the user full access to all aspects of the workflow. | command line, workflow, bioinformatics | is listed by: OMICtools | GNU General Public License, v3 | OMICS_01144 | SCR_005373 | 2026-09-19 12:50:52 | 0 | ||||||||
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AGE Resource Report Resource Website 1+ mentions |
AGE (RRID:SCR_005253) | AGE | software resource | A tool that implements an algorithm for optimal alignment of sequences with Structural Variations (SVs). | genome |
is listed by: OMICtools has parent organization: Yale University; Connecticut; USA |
OMICS_00305 | SCR_005253 | 2026-09-19 12:50:50 | 3 | |||||||||
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EBIMed Resource Report Resource Website 1+ mentions |
EBIMed (RRID:SCR_005314) | EBIMed | service resource | A web application that combines Information Retrieval and Extraction from Medline. EBIMed finds Medline abstracts in the same way PubMed does. Then it goes a step beyond and analyses them to offer a complete overview on associations between UniProt protein/gene names, GO annotations, Drugs and Species. The results are shown in a table that displays all the associations and links to the sentences that support them and to the original abstracts. By selecting relevant sentences and highlighting the biomedical terminology EBIMed enhances your ability to acquire knowledge, relate facts, discover implications and, overall, have a good overview economizing the effort in reading. | protein, gene, annotation, drug, specie, association, database |
is listed by: OMICtools is related to: MEDLINE is related to: PubMed is related to: Gene Ontology is related to: UniProt is related to: NCBI Taxonomy is related to: MedlinePlus has parent organization: European Bioinformatics Institute |
OMICS_01180 | SCR_005314 | 2026-09-19 12:50:51 | 1 | |||||||||
|
Bio-Linux Resource Report Resource Website 10+ mentions |
Bio-Linux (RRID:SCR_005399) | Bio-Linux | software resource | A free, fully featured, powerful, configurable and easy to maintain bioinformatics workstation that provides more than 500 bioinformatics programs on an Ubuntu Linux 12.04 LTS base. Install it or run it live. There is a graphical menu for bioinformatics programs, as well as easy access to the Bio-Linux bioinformatics documentation system and sample data useful for testing programs. You can run a Bio-Linux system on Amazon EC2 or other cloud computing architectures by using CloudBioLinux. | ubuntu, cloud computing, workstation, bioinformatics |
is recommended by: NERC Environmental Bioinformatics Centre is listed by: OMICtools has parent organization: Natural Environment Research Council |
PMID:16841067 | Acknowledgement requested, Open unspecified license | OMICS_01137 | SCR_005399 | BioLinux, NEBC Bio-Linux | 2026-09-19 12:50:53 | 33 | ||||||
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G-Mo.R-Se Resource Report Resource Website 1+ mentions |
G-Mo.R-Se (RRID:SCR_005273) | G-Mo.R-Se | software resource | Software aimed at using RNA-Seq short reads to build de novo gene models. First, candidate exons are built directly from the positions of the reads mapped on the genome (without any ab initio assembly of the reads), and all the possible splice junctions between those exons are tested against unmapped reads : the testing of junctions is directed by the information available in the RNA-Seq dataset rather than a priori knowledge about the genome. Exons can thus be chained into stranded gene models. | bio.tools, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
OMICS_01259, biotools:g-mo.r-se, biotools:gmorse | https://bio.tools/g-mo.r-se, https://bio.tools/gmorse | SCR_005273 | Gene MOdeling using RNA-Seq, G-Mo.R-Se: Gene MOdeling using RNA-Seq | 2026-09-19 12:50:50 | 1 | |||||||
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Binding and Expression Target Analysis Resource Report Resource Website 100+ mentions |
Binding and Expression Target Analysis (RRID:SCR_005396) | BETA | analysis service resource, data analysis service, production service resource, service resource, software resource | A software package that integrates ChIP-seq of transcription factors or chromatin regulators with differential gene expression data to infer direct target genes. BETA has three functions: (1) to predict whether the factor has activating or repressive function; (2) to infer the factor''''s target genes; and (3) to identify the motif of the factor and its collaborators which might modulate the factor''''s activating or repressive function. BETA requires ~2GB RAM and 1h for the whole procedure. BETA may run on the web server at Cistrome or may be downloaded. | transcription factor, chromatin regulator, transcriptome, chip-seq, cistrome, gene expression, target gene, motif, differential gene expression |
is listed by: OMICtools is related to: Galaxy |
PMID:24263090 | Registration required, Open unspecified license | OMICS_00515 | SCR_005396 | BETA - Binding and Expression Target Analysis | 2026-09-19 12:50:52 | 455 | ||||||
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SysCall Resource Report Resource Website 1+ mentions |
SysCall (RRID:SCR_005307) | SysCall | software resource | A logistic regression based classifier distinguishing heterozygous sites from systematic errors. Given a list of candidate heterozygous genomic locations and a sam file of sequenced reads SysCall classifies each genomic location as either a heterozygous site or a systematic error and outputs according lists, along with the assigned posterior probabilities. | high-throughput sequencing |
is listed by: OMICtools has parent organization: University of California at Berkeley; Berkeley; USA |
PMID:22099972 | Acknowledgement requested, Registration required | OMICS_01080 | SCR_005307 | SysCall - Distinguishing heterozygous sites from systematic errors | 2026-09-19 12:50:51 | 2 | ||||||
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inGAP Resource Report Resource Website 10+ mentions |
inGAP (RRID:SCR_005261) | inGAP | software resource | Software mining pipeline guided by a Bayesian principle to detect single nucleotide polymorphisms, insertion and deletions by comparing high-throughput pyrosequencing reads with a reference genome of related organisms. This pipeline is extended to identify and visualize large-size structural variations, including insertions, deletions, inversions and translocations. | structural variation, genome, next-generation sequence, genome analysis, alignment, single nucleotide polymorphism, insertion, deletion, indel, inversion, translocation, windows, linux, macos/x, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge has parent organization: Fudan University; Shanghai; China has parent organization: Chinese Academy of Sciences; Beijing; China |
OMICS_00319, biotools:ingap | https://bio.tools/ingap | SCR_005261 | inGAP-sv, inGAP-sv: structural variation detection and visualization, integrative next-generation genome analysis pipeline | 2026-09-19 12:50:50 | 29 | |||||||
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PEMer Resource Report Resource Website 1+ mentions |
PEMer (RRID:SCR_005263) | software resource | Software package as computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data. Package is composed of three modules, PEMer workflow, SV-Simulation and BreakDB. PEMer workflow is a sensitive software for detecting SVs from paired-end sequence reads. SV-Simulation randomly introduces SVs into a given genome and generates simulated paired-end reads from novel genome. | structural variation, genome, next-generation sequencing, bio.tools, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: BreakDB has parent organization: European Molecular Biology Laboratory |
PMID:19236709 | biotools:pemer, OMICS_00320 | https://bio.tools/pemer, https://bio.tools/pemer | SCR_005263 | Paired-End Mapper | 2026-09-19 12:50:50 | 7 | |||||||
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phantompeakqualtools Resource Report Resource Website 50+ mentions |
phantompeakqualtools (RRID:SCR_005331) | phantompeakqualtools | software resource | Software package that computes quick but highly informative enrichment and quality measures for ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data. It can also be used to obtain robust estimates of the predominant fragment length or characteristic tag shift values in these assays. | chip-seq, dnase-seq, faire-seq, mnase-seq, dataquality, enrichment, phantompeak, cross-correlation, spppeakcaller, chipseq, dnaseseq, fairseq, mnaseseq, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Google Code |
MIT License | biotools:phantompeakqualtools, OMICS_00431 | https://bio.tools/phantompeakqualtools | SCR_005331 | phantompeakqualtools - Computes quick but highly informative enrichment and quality measures and fragment lengths for ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data | 2026-09-19 12:50:51 | 87 | ||||||
|
CoIN Resource Report Resource Website 100+ mentions |
CoIN (RRID:SCR_005332) | CoIN | service resource | A web-based system that assess articles according to their term correlations among sentences. It employs the co-occurrence relations and their network centralities to evaluate the influence of biomedical terms from Comparative Toxicogenomics Database (CTD)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene, disease, chemical, biomedical, association, document triage, database, FASEB list |
is listed by: OMICtools has parent organization: National Cheng Kung University; Tainan; Taiwan |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01177 | SCR_005332 | Co-occurrence Interaction Nexus, CoIN: A network exploration for document triage, CoIN: Co-occurrence Interaction Nexus | 2026-09-19 12:50:51 | 138 | |||||||
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ABS filter Resource Report Resource Website |
ABS filter (RRID:SCR_005328) | ABS filter | software resource | R package for identification and removal of low-complexity sites in allele-specific analysis of ChIP-seq data. | unix/linux |
is listed by: OMICtools has parent organization: Ecole Polytechnique Federale de Lausanne; Lausanne; Switzerland |
PMID:24255646 | GNU General Public License, v3 | OMICS_00427 | SCR_005328 | R package - ABS filter, absfilter | 2026-09-19 12:50:51 | 0 | ||||||
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SeqWare Resource Report Resource Website 10+ mentions |
SeqWare (RRID:SCR_005289) | SeqWare | software resource | A portable software infrastructure designed to analyze massive genomics datasets produced by contemporary and emerging technologies, in particular Next Generation Sequencing (NGS) platforms. It consists of a comprehensive suite of infrastructure tools focused on enabling the end-to-end analysis of sequence data ? from from raw base calling to analyzed variants ready for interpretation by users. SeqWare is tool agnostic, it is a framework for building analysis workflows and does not provide specific implementations out-of-the-box. You use SeqWare to create high-throughput infrastructure for NGS analysis using whatever analysis tools you like. SeqWare currently provides 5 main tools specifically designed to support massively parallel sequencing technologies. All tools can be used together or separately: * MetaDB: provides a common database to store metadata used by all components. * Portal: a LIMS-like web application to manage samples, record computational events, and present results back to end users. * Pipeline: a workflow engine that is capable of wrapping and combining other tools (BFAST, BWA, SAMtools, etc) into complex pipelines, recording metadata about the analysis, and facilitates automation of pipelines based on metadata. * Web Service: a programmatic API that lets people build new tools on top of the project * Query Engine: a NoSQL database designed to store and query variants and other events inferred from sequence data. | mapreduce/hadoop, next generation sequencing, genomics | is listed by: OMICtools | PMID:21210981 | Acknowledgement requested, GNU General Public License, v3 | OMICS_01221 | SCR_005289 | SolexaTools | 2026-09-19 12:50:51 | 13 | ||||||
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Coremine Medical Resource Report Resource Website 1+ mentions |
Coremine Medical (RRID:SCR_005323) | Coremine Medical | service resource | Service to access comprehensive information on diseases, drugs, treatments and medical biology. It is ideal for those seeking an overview of a complex subject while allowing the possibility to drill down to specific details. Search results are presented in a dashboard format comprized of panels containing various categories of information ranging from introductory sources to the latest scientific articles. | disease, drug, treatment, medical biology, text mining, health, medicine, biology, network, database |
is listed by: OMICtools is related to: MeSH is related to: Entrez Gene is related to: MEDLINE is related to: PubMed is related to: DrugBank is related to: Gene Ontology is related to: UniProt has parent organization: PubGene |
NLM ; European Union FP7 ; Research Council of Norway ; Innovation Norway |
Copyrighted | OMICS_01179 | SCR_005323 | 2026-09-19 12:50:51 | 6 | |||||||
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CoverageCalculator Resource Report Resource Website 1+ mentions |
CoverageCalculator (RRID:SCR_005352) | CoverageCalculator | software resource | Small and very fast utility to calculate X-coverage from Next-Generation-Sequencing data. | next-generation sequencing |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_01164 | SCR_005352 | 2026-09-19 12:50:52 | 2 | |||||||||
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WHAM Resource Report Resource Website 100+ mentions |
WHAM (RRID:SCR_005497) | WHAM | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. High-throughput sequence alignment tool that aligns short DNA sequences (reads) to the whole human genome at a rate of over 1500 million 60bps reads per hour, which is one to two orders of magnitudes faster than the leading state-of-the-art techniques. Feature list for the current version (v 0.1.5) of WHAM: * Supports paired-end reads * Supports up to 5 errores * Supports alignments with gaps * Supports quality scores for filtering invalid alignments, and sorting valid alignments * finds ALL valid alignments * Supports multi-threading * Supports rich reporting modes * Supports SAM format output | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University of Wisconsin-Madison; Wisconsin; USA |
Facebook ; NSF IIS-1110948 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00697, biotools:wham | https://bio.tools/wham, https://sources.debian.org/src/wham-align/ | SCR_005497 | Wisconsin?s High-throughput Alignment Method | 2026-09-19 12:50:54 | 345 | |||||
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FLASH Resource Report Resource Website 1000+ mentions |
FLASH (RRID:SCR_005531) | FLASh | data analysis software, data processing software, sequence analysis software, software application, software resource | Open source software tool to merge paired-end reads from next-generation sequencing experiments. Designed to merge pairs of reads when original DNA fragments are shorter than twice length of reads. Can improve genome assemblies and transcriptome assembly by merging RNA-seq data. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: shovill is related to: CLIP-Explorer has parent organization: Johns Hopkins University; Maryland; USA |
NHGRI R01 HG006677; NIGMS R01 GM083873; NLM R01 LM006845 |
PMID:21903629 | Free, Available for download, Freely available | biotools:flash, OMICS_01047 | https://sourceforge.net/projects/flashpage/files/, https://bio.tools/flash, https://sources.debian.org/src/flash/ | SCR_005531 | Fast Length Adjustment of SHort reads, Fast Length Adjustment of Short reads | 2026-09-19 12:50:55 | 2461 | ||||
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SeqMap Resource Report Resource Website 50+ mentions |
SeqMap (RRID:SCR_005495) | SeqMap | software resource | A software tool for mapping large amount of oligonucleotide to the genome. It is designed for finding all the places in a genome where an oligonucleotide could potentially come from. SeqMap can efficiently map as many as dozens of millions of short sequences to a genome of several billions of nucleotides. While doing the mapping, several mutations as well as insertions / deletions of the nucleotide bases in the sequences can be tolerated and furthermore detected. Various input and output formats are supported, as well as many command line options for tuning almost every steps in the mapping process. A typical mapping can be done in a few hours on an ordinary PC. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University of Michigan; Ann Arbor; USA |
PMID:18697769 | Free, Non-commercial, Commercial use requires permission | biotools:seqmap, OMICS_00684 | https://bio.tools/seqmap | SCR_005495 | SeqMap - A Tool For Mapping Millions Of Short Sequences To The Genome | 2026-09-19 12:50:54 | 97 | |||||
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Jellyfish Resource Report Resource Website 1000+ mentions |
Jellyfish (RRID:SCR_005491) | Jellyfish | software resource | A software tool for fast, memory-efficient counting of k-mers in DNA. A k-mer is a substring of length k, and counting the occurrences of all such substrings is a central step in many analyses of DNA sequence. JELLYFISH can count k-mers quickly by using an efficient encoding of a hash table and by exploiting the compare-and-swap CPU instruction to increase parallelism. Jellyfish is a command-line program that reads FASTA and multi-FASTA files containing DNA sequences. It outputs its k-mer counts in an binary format, which can be translated into a human-readable text format using the jellyfish dump command., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | c++, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University of Maryland; Maryland; USA |
PMID:21217122 DOI:10.1093/bioinformatics/btr011 |
THIS RESOURCE IS NO LONGER IN SERVICE | biotools:jellyfish, OMICS_01056 | https://bio.tools/jellyfish, https://sources.debian.org/src/jellyfish1/ | SCR_005491 | Jellyfish mer counter | 2026-09-19 12:50:54 | 1134 |
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