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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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ACT: Artemis Comparison Tool Resource Report Resource Website 10+ mentions |
ACT: Artemis Comparison Tool (RRID:SCR_004507) | ACT | software resource | A free tool for displaying pairwise comparisons between two or more DNA sequences. It can be used to identify and analyze regions of similarity and difference between genomes and to explore conservation of synteny, in the context of the entire sequences and their annotation. It is based on the software for Artemis, the genome viewer and annotation tool. ACT runs on UNIX, GNU/Linux, Macintosh and MS Windows systems. It can read complete EMBL and GENBANK entries or sequences in FASTA or raw format. Other sequence features can be in EMBL, GENBANK or GFF format. | dna sequence, genome, synteny, pairwise comparison |
is listed by: OMICtools has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
Wellcome Trust | PMID:15976072 | GNU General Public License | OMICS_00928, nlx_48986 | SCR_004507 | Artemis Comparison Tool | 2026-02-14 02:00:44 | 46 | |||||
|
VariationHunter Resource Report Resource Website 10+ mentions |
VariationHunter (RRID:SCR_004865) | VariationHunter | software resource | A software tool for discovery of structural variation in one or more individuals simultaneously using high throughput technologies. | structural variation, genome, next-generation sequencing |
is listed by: OMICtools is related to: SPLITREAD has parent organization: Simon Fraser University; British Columbia; Canada has parent organization: SourceForge |
PMID:22048523 PMID:20529927 |
OMICS_00328 | SCR_004865 | VariationHunter-CommonLaw | 2026-02-14 02:00:46 | 12 | |||||||
|
Phymm and PhymmBL Resource Report Resource Website 10+ mentions |
Phymm and PhymmBL (RRID:SCR_004751) | Phymm, PhymmBL | software resource | Software for Phylogenetic Classification of Metagenomic Data with Interpolated Markov Models to taxonomically classify DNA sequences and accurately classify reads as short as 100 bp. PhymmBL, the hybrid classifier included in this distribution which combines analysis from both Phymm and BLAST, produces even higher accuracy. | metagenome, sequence, taxonomy, classification, phylogenetic classification, genome, short read |
is listed by: OMICtools has parent organization: University of Maryland; Maryland; USA |
NLM R01-LM006845 | PMID:19648916 PMID:21527926 |
Open-source license | OMICS_01461 | SCR_004751 | 2026-02-14 02:00:44 | 12 | ||||||
|
deStruct Resource Report Resource Website 1+ mentions |
deStruct (RRID:SCR_004747) | deStruct | software resource | A software tool for identifying structural variation in tumour genomes from whole genome illumina sequencing. | structural variation, genome, genomics |
is listed by: OMICtools has parent organization: Google Code |
Tumor, Cancer | Open unspecified license | OMICS_00314 | SCR_004747 | deStruct - Bioinformatics tool for identifying structural variation in tumour genomes | 2026-02-14 02:00:59 | 7 | ||||||
|
SSPACE Resource Report Resource Website 100+ mentions |
SSPACE (RRID:SCR_005056) | SSPACE | software resource | A stand-alone software program for scaffolding pre-assembled contigs using paired-read data. Main features are: a short runtime, multiple library input of paired-end and/or mate pair datasets and possible contig extension with unmapped sequence reads. | scaffolding, contig, genome, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:21149342 DOI:10.1093/bioinformatics/btq683 |
GNU General Public License, Registration required | biotools:sspace, OMICS_00050 | https://bio.tools/sspace https://sources.debian.org/src/sspace/ |
SCR_005056 | 2026-02-14 02:01:02 | 426 | ||||||
|
AGORA Resource Report Resource Website 50+ mentions |
AGORA (RRID:SCR_005070) | AGORA | software resource | An algorithm to use optical map information directly within the de Bruijn graph framework to help produce an accurate assembly of a genome that is consistent with the optical map information provided. AGORA takes as input two data structures: OpMap ? an ordered list of fragment sizes representing the optical map; and Edges ? a list of de Bruijn graph edges with their corresponding sequences. | genome assembly, genome, reconstruction | is listed by: OMICtools | PMID:22856673 | OMICS_00039 | SCR_005070 | Assembly Guided by Optical Restriction Alignment | 2026-02-14 02:01:03 | 99 | |||||||
|
RetroSeq Resource Report Resource Website 10+ mentions |
RetroSeq (RRID:SCR_005133) | RetroSeq | software resource | A tool for discovery and genotyping of transposable element variants (TEVs) (also known as mobile element insertions) from next-gen sequencing reads aligned to a reference genome in BAM format. The goal is to call TEVs that are not present in the reference genome but present in the sample that has been sequenced. It should be noted that RetroSeq can be used to locate any class of viral insertion in any species where whole-genome sequencing data with a suitable reference genome is available. RetroSeq is a two phase process, the first being the read pair discovery phase where discorandant mate pairs are detected and assigned to a TE class (Alu, SINE, LINE, etc.) by using either the annotated TE elements in the reference and/or aligned with Exonerate to the supplied library of viral sequences. | mobile element insertion, next-gen sequencing, bam, transposable element, genome, sequence |
is listed by: OMICtools has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
PMID:23233656 | Acknowledgement requested, Open unspecified license | OMICS_11232, OMICS_00120 | SCR_005133 | 2026-02-14 02:00:51 | 45 | |||||||
|
VirusFinder Resource Report Resource Website 10+ mentions |
VirusFinder (RRID:SCR_005205) | VirusFinder | software resource | Software tool for efficient and accurate detection of viruses and their integration sites in host genomes through next generation sequencing data. Specifically, it detects virus infection, co-infection with multiple viruses, virus integration sites in host genomes, as well as mutations in the virus genomes. It also facilitates virus discovery by reporting novel contigs, long sequences assembled from short reads that map neither to the host genome nor to the genomes of known viruses. VirusFinder 2 works with both paired-end and single-end data, unlike the previous 1.x versions that accepted only paired-end reads. The types of NGS data that VirusFinder 2 can deal with include whole genome sequencing (WGS), whole transcriptome sequencing (RNA-Seq), targeted sequencing data such as whole exome sequencing (WES) and ultra-deep amplicon sequencing. | next-generation sequencing, virus, integration site, genome, mutation, virus genome, contig, paired-end, single-end, whole genome sequencing, whole transcriptome sequencing, rna-seq, targeted sequencing, whole exome sequencing, ultra-deep amplicon sequencing |
is listed by: OMICtools has parent organization: Vanderbilt University; Tennessee; USA |
Viral infection | PMID:23717618 | OMICS_00226 | SCR_005205 | 2026-02-14 02:01:05 | 16 | |||||||
|
NGS-SNP Resource Report Resource Website 10+ mentions |
NGS-SNP (RRID:SCR_005182) | NGS-SNP | software resource | A collection of command-line scripts for providing rich annotations for SNPs identified by the sequencing of transcripts or whole genomes from organisms with reference sequences in Ensembl. Included among the annotations, several of which are not available from any existing SNP annotation tools, are the results of detailed comparisons with orthologous sequences. These comparisons allow, for example, SNPs to be sorted or filtered based on how drastically the SNP changes the score of a protein alignment. Other fields indicate the names of overlapping protein domains or features, and the conservation of both the SNP site and flanking regions. NCBI, Ensembl, and Uniprot IDs are provided for genes, transcripts, and proteins when applicable, along with Gene Ontology terms, a gene description, phenotypes linked to the gene, and an indication of whether the SNP is novel or known. A ?Model_Annotations? field provides several annotations obtained by transferring in silico the SNP to an orthologous gene, typically in a well-characterized species. | annotation, snp, sequencing, transcript, genome, reference sequence, indel, annotate, reference chromosome, reference transcript, gene, command-line |
is listed by: OMICtools is related to: Ensembl has parent organization: University of Alberta; Alberta; Canada |
OMICS_00177 | SCR_005182 | 2026-02-14 02:00:50 | 32 | |||||||||
|
SVDetect Resource Report Resource Website 10+ mentions |
SVDetect (RRID:SCR_010812) | SVDetect | software resource | Software application for the isolation and the type prediction of intra- and inter-chromosomal rearrangements from paired-end/mate-pair sequencing data provided by the high-throughput sequencing technologies. This tool aims to identify structural variations with both clustering and sliding-window strategies, and helping in their visualization at the genome scale. It is compatible with SOLiD and Illumina (>=1.3) reads. | structural variation, sequencing, chromosomal rearrangement, high-throughput sequencing, solid, illumina, genome, insertion, deletion, inversion, duplication, translocation, command-line, perl, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge has parent organization: Curie Institute; Paris; France |
PMID:20639544 | GNU General Public License, v3 | OMICS_00324, biotools:svdetect | https://bio.tools/svdetect | SCR_010812 | SVDetect: a tool to detect genomic structural variations from paired-end and mate-pair sequencing data | 2026-02-14 02:01:50 | 23 | |||||
|
IGB Resource Report Resource Website 100+ mentions |
IGB (RRID:SCR_011792) | IGB | software resource | An easy-to-use, highly customizable genome browser you can use to visualize and explore genomic data and annotations, including RNA-Seq, ChIP-Seq, tiling array data, and more. | genome, rna-seq, chip-seq, tiling array, browser |
is listed by: OMICtools has parent organization: University of North Carolina at Charlotte; North Carolina; USA |
PMID:19654113 | Free, Acknowledgement requested | OMICS_00916 | SCR_011792 | Integrated Genome Browser | 2026-02-14 02:02:26 | 336 | ||||||
|
GenomeJack Resource Report Resource Website 10+ mentions |
GenomeJack (RRID:SCR_012026) | GenomeJack | software resource | A genome browser specialized in next-generation sequencing data. | next-generation sequencing, genome, browser, analysis | is listed by: OMICtools | Free, Public | OMICS_02143 | SCR_012026 | 2026-02-14 02:02:17 | 32 | ||||||||
|
Ergatis Resource Report Resource Website 1+ mentions |
Ergatis (RRID:SCR_005377) | Ergatis | software resource | A web interface and scalable software system for bioinformatics workflows that is used to create, run, and monitor reusable computational analysis pipelines. It contains pre-built components for common bioinformatics analysis tasks. These components can be arranged graphically to form highly-configurable pipelines. Each analysis component supports multiple output formats, including the Bioinformatic Sequence Markup Language (BSML). The current implementation includes support for data loading into project databases following the CHADO schema, a highly normalized, community-supported schema for storage of biological annotation data. Ergatis uses the Workflow engine to process its work on a compute grid. Workflow provides an XML language and processing engine for specifying the steps of a computational pipeline. It provides detailed execution status and logging for process auditing, facilitates error recovery from point of failure, and is highly scalable with support for distributed computing environments. The XML format employed enables commands to be run serially, in parallel, and in any combination or nesting level. | workflow, bioinformatics, workflow management, pipeline, computation, genomics, genome, processing |
is listed by: OMICtools has parent organization: SourceForge has parent organization: University of Maryland School of Medicine; Maryland; USA |
PMID:20413634 | Artistic License | OMICS_01140 | SCR_005377 | ergatis: workflow creation and monitoring interface | 2026-02-14 02:01:05 | 2 | ||||||
|
CREST Resource Report Resource Website 50+ mentions |
CREST (RRID:SCR_005257) | CREST | software resource | An algorithm for detecting genomic structural variations at base-pair resolution using next-generation sequencing data. CREST uses pieces of DNA called soft clips to find structural variations. Soft clips are the DNA segments produced during sequencing that fail to properly align to the reference genome as the sample genome is reassembled. CREST uses the soft clips to precisely identify sites of chromosomal rearrangement or where pieces of DNA are inserted or deleted. | genome, structural variation, next-generation sequencing, soft clip |
is listed by: OMICtools has parent organization: Pennsylvania State University |
PMID:21666668 | OMICS_00312 | SCR_005257 | 2026-02-14 02:00:51 | 54 | ||||||||
|
MolBioLib Resource Report Resource Website |
MolBioLib (RRID:SCR_005372) | MolBioLib | software resource | A compact, portable, and extensively tested C++11 software framework and set of applications tailored to the demands of next-generation sequencing data and applicable to many other applications. It is designed to work with common file formats and data types used both in genomic analysis and general data analysis. A central relational-database-like Table class is a flexible and powerful object to intuitively represent and work with a wide variety of tabular datasets, ranging from alignment data to annotations. MolBioLib includes programs to perform a wide variety of analysis tasks such as computing read coverage, annotating genomic intervals, and novel peak calling with a wavelet algorithm. This package assumes fluency in both UNIX and C++. | c++, next-generation sequencing, genomic, analysis, genome |
is listed by: OMICtools has parent organization: SourceForge |
PMID:22815363 | OMICS_01145 | SCR_005372 | MolBioLib: C++11 framework for rapid develop and deploy of bioinformatic tasks | 2026-02-14 02:00:53 | 0 | |||||||
|
BioExtract Resource Report Resource Website 10+ mentions |
BioExtract (RRID:SCR_005397) | BioExtract | service resource | An open, web-based system designed to aid researchers in the analysis of genomic data by providing a platform for the creation of bioinformatic workflows. Scientific workflows are created within the system by recording tasks performed by the user. These tasks may include querying multiple, distributed data sources, saving query results as searchable data extracts, and executing local and web-accessible analytic tools. The series of recorded tasks can then be saved as a reproducible, sharable workflow available for subsequent execution with the original or modified inputs and parameter settings. Integrated data resources include interfaces to the National Center for Biotechnology Information (NCBI) nucleotide and protein databases, the European Molecular Biology Laboratory (EMBL-Bank) non-redundant nucleotide database, the Universal Protein Resource (UniProt), and the UniProt Reference Clusters (UniRef) database. The system offers access to numerous preinstalled, curated analytic tools and also provides researchers with the option of selecting computational tools from a large list of web services including the European Molecular Biology Open Software Suite (EMBOSS), BioMoby, and the Kyoto Encyclopedia of Genes and Genomes (KEGG). The system further allows users to integrate local command line tools residing on their own computers through a client-side Java applet. | nucleotide sequence, protein sequence, viridiplantae, viridiplantae protein, nucleotide, sequence, protein, viridiplantae, workflow, software, database, bioinformatics, platform, genome, genomic analysis, analytic tool |
is listed by: OMICtools is listed by: SoftCite is related to: NCBI Nucleotide is related to: NCBI Protein Database is related to: UniProt is related to: UniRef is related to: EMBOSS is related to: BioMoby is related to: KEGG has parent organization: Indiana University; Indiana; USA has parent organization: University of South Dakota; South Dakota; USA |
NSF 0090732; NSF IOS-1126481 |
PMID:21546552 PMID:20865520 PMID:20150665 PMID:20054995 |
OMICS_01138 | SCR_005397 | BioExtract Server | 2026-02-14 02:00:53 | 11 | ||||||
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SPLITREAD Resource Report Resource Website 1+ mentions |
SPLITREAD (RRID:SCR_005264) | SPLITREAD | software resource | Software for detecting INDELs (small insertions and deletion with size less than 50bp) as well as large deletions that are within the coding regions from the exome sequencing data. It also can be applied to the whole genome sequencing data. | deletion, insertion, indel, genome, exome |
is listed by: OMICtools is related to: drFAST is related to: mrFAST is related to: mrsFAST is related to: VariationHunter is related to: NovelSeq is related to: mrCaNaVaR has parent organization: SourceForge |
OMICS_00323 | SCR_005264 | SPLITREAD - Split read based INDEL/SV Caller | 2026-02-14 02:00:53 | 3 | ||||||||
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Hydra Resource Report Resource Website 100+ mentions |
Hydra (RRID:SCR_005260) | Hydra | software resource | Software that detects structural variation (SV) breakpoints by clustering discordant paired-end alignments whose signatures corroborate the same putative breakpoint. Hydra can detect breakpoints caused by all classes of structural variation. Moreover, it was designed to detect variation in both unique and duplicated genomic regions; therefore, it will examine paired-end reads having multiple discordant alignments. Hydra does not attempt to classify SV breakpoints based on the mapping distances and orientations of each breakpoint cluster, it merely detects and reports breakpoints. This is an intentional decision, as it was observed that in loci affected by complex rearrangements, the type of variant suggested by the breakpoint signature is not always correct. Hydra does report the orientations, distances, number of supporting read-pairs, etc., for each breakpoint. It is suggested that downstream methods be used to classify variants based on the genomic features that they overlap and the co-occurrence of other breakpoints. For example, they developed BEDTools for exactly this purpose and the breakpoints reported by Hydra are in the BEDPE format used by BEDTools. Future releases of Hydra will include scripts that assist in the classification process. | structural variation, genome, genomic, breakpoint, c++, cnv, pem, paired-end, segmental duplication, rearrangement |
is listed by: OMICtools is listed by: SoftCite is related to: BEDTools has parent organization: Google Code has parent organization: University of Virginia; Virginia; USA |
OMICS_00318 | SCR_005260 | hydra-sv | 2026-02-14 02:01:05 | 115 | ||||||||
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GEM Resource Report Resource Website 10+ mentions |
GEM (RRID:SCR_005339) | GEM | software resource | Java software for studying protein-DNA interaction using ChIP-seq / ChIP-exo data. It links binding event discovery and motif discovery with positional priors in the context of a generative probabilistic model of ChIP data and genome sequence, resolves ChIP data into explanatory motifs and binding events at unsurpassed spatial resolution. GEM reciprocally improves motif discovery using binding event locations, and binding event predictions using discovered motifs. | chip-seq, chip-exo, genome, event, motif, protein-dna interaction, java, transcription factor, genome sequence, motif discovery, binding event calling |
is listed by: OMICtools has parent organization: Massachusetts Institute of Technology; Massachusetts; USA; |
PMID:22912568 | OMICS_00441 | SCR_005339 | Genome wide Event finding and Motif discovery, GEM: ChIP-Seq and ChIP-exo analysis tool | 2026-02-14 02:00:52 | 12 | |||||||
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Fulcrum Resource Report Resource Website 1+ mentions |
Fulcrum (RRID:SCR_005523) | Fulcrum | software resource | Software to collapse identical and near-identical Illumina and 454 reads (such as those from PCR clones) into single error-corrected sequences; it can process paired-end as well as single-end reads. Fulcrum is customizable and can be deployed on a single machine, a local network or a commercially available MapReduce cluster, and it has been optimized to maximize ease-of-use, cross-platform compatibility and future scalability. Sequence datasets have been collapsed by up to 71%, and the reduced number and improved quality of the resulting sequences allow assemblers to produce longer contigs while using less memory. | illumina, 454, read, paired-end read, single-end read, high-throughput sequencing, redundant read, genome, transcriptome, ultra high throughput sequencing |
is listed by: OMICtools has parent organization: Stanford University School of Medicine; California; USA |
PMID:22419786 | BSD-like license | OMICS_01049 | http://pringlelab.stanford.edu/protocols.html | SCR_005523 | Fulcrum Read Collapser | 2026-02-14 02:01:08 | 4 |
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