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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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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 | 2026-08-01 12:02:58 | 1 | |||||||||
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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 | 2026-08-01 12:02:51 | 1 | |||||||
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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 | 2026-08-01 12:02:52 | 2 | ||||||
|
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 | 2026-08-01 12:02:49 | 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 | 2026-08-01 12:02:51 | 7 | |||||||
|
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 | 2026-08-01 12:02:52 | 86 | ||||||
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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 | 2026-08-01 12:02:58 | 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 | 2026-08-01 12:02:52 | 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 | 2026-08-01 12:02:58 | 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 | 2026-08-01 12:02:50 | 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 | 2026-08-01 12:02:52 | 2 | |||||||||
|
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 | 2026-08-01 12:02:55 | 345 | |||||
|
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 | 2026-08-01 12:02:59 | 95 | |||||
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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 | 2026-08-01 12:02:59 | 1130 | |||||
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FreClu Resource Report Resource Website |
FreClu (RRID:SCR_005524) | FreClu | software resource | An algorithm for efficient frequency-based de novo short read clustering for error trimming in next-generation sequencing. It organizes erroneous short sequences originating in a single abundant sequence into a tree structure such that each child sequence is considered to be derived stochastically from its more abundant parent sequence because of sequencing errors. | next-generation sequencing |
is listed by: OMICtools has parent organization: University of Tokyo; Tokyo; Japan |
OMICS_01048 | SCR_005524 | FreClu - Efficient Frequency-based de Novo Short Read Clustering | 2026-08-01 12:03:00 | 0 | ||||||||
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mrFAST Resource Report Resource Website 10+ mentions |
mrFAST (RRID:SCR_005487) | mrFAST | software resource | Software designed to map short reads generated with the Illumina platform to reference genome assemblies; in a fast and memory-efficient mannerl. Currently Supported Features: * Output in SAM format * Indels up to 8 bp (4 bp deletions and 4 bp insertions) * Paired-end mapping ** Discordant option to generate mapping file ready for VariationHunter to detect structural variants. * One end anchored (OEA) map locations for novel sequence insertion detection with NovelSeq * Matepair library mapping (long inserts with RF orientation). Planned Features: * Multithreading | next-generation sequencing, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: SPLITREAD has parent organization: SourceForge |
PMID:19718026 | biotools:mrfast, OMICS_00671 | https://bio.tools/mrfast | SCR_005487 | mrFAST - Micro Read Fast Alignment Search Tool, Micro Read Fast Alignment Search Tool | 2026-08-01 12:02:54 | 16 | ||||||
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GNUMAP Resource Report Resource Website 1+ mentions |
GNUMAP (RRID:SCR_005482) | GNUMAP | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 3rd,2023. A software program designed to accurately map sequence data obtained from next-generation sequencing machines (specifically that of Solexa/Illumina) back to a genome of any size. By using the posterior probability of mapping a given read to a specific genomic loation, we are able to account for repetitive reads by distributing them across several regions in the genome. In addition, the output of the program is created in such a way that it can be easily viewed through other free and readily- available programs. Several benchmark data sets were created with spiked-in duplicate regions, and GNUMAP was able to more accurately account for these duplicate regions. | next-generation sequencing, genome, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Brigham Young University; Utah; USA |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00664, biotools:gnumap | https://bio.tools/gnumap | SCR_005482 | Genomic Next-generation Universal MAPper | 2026-08-01 12:02:53 | 7 | ||||||
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Kraken Resource Report Resource Website 1000+ mentions |
Kraken (RRID:SCR_005484) | Kraken | software resource | A set of software tools ( Reaper, Tally and Sequence Imp) designed to streamline the analysis of next-generation sequencing data. Although designed with small RNA sequence analysis in mind the tools can be used to address issues facing next-generation sequencing in general. | adapter trimming, algorithm, next-generation sequencing, pipeline, rnaseq, sequencing |
is listed by: OMICtools has parent organization: European Bioinformatics Institute |
PMID:23816787 | Apache License | OMICS_01057 | SCR_005484 | Kraken: A set of tools for quality control and analysis of high-throughput sequence data | 2026-08-01 12:02:54 | 1711 | ||||||
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CUSHAW2-GPU Resource Report Resource Website |
CUSHAW2-GPU (RRID:SCR_005480) | CUSHAW2-GPU | software resource | Software program (based on CUSHAW2) designed and optimized for Kepler-based GPUs, but still workable on earlier-generation Fermi-based ones. | c++, genome, alignment |
is listed by: OMICtools is related to: CUSHAW has parent organization: SourceForge |
Apache License | OMICS_00659 | SCR_005480 | 2026-08-01 12:02:59 | 0 | ||||||||
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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 | 2026-08-01 12:02:53 | 32 |
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