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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
USeq Resource Report Resource Website 100+ mentions |
USeq (RRID:SCR_004753) | USeq | software resource | A collection of software tools for for both low and high level analysis of next generation, ultra high throughput signature sequencing data from the Solexa, SOLiD, and 454 platforms. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
OMICS_00499, biotools:useq | https://bio.tools/useq | SCR_004753 | 2026-09-12 12:56:16 | 131 | ||||||||
|
NCBI BLAST Resource Report Resource Website 10000+ mentions |
NCBI BLAST (RRID:SCR_004870) | BLAST | data access protocol, data analysis software, data processing software, sequence analysis software, software application, software resource, web service | Web search tool to find regions of similarity between biological sequences. Program compares nucleotide or protein sequences to sequence databases and calculates statistical significance. Used for identifying homologous sequences. | genome, similarity, sequence, nucleotide, protein, gene, data, bio.tools |
is used by: MITE-Tracker is used by: Cello2Go is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: G-BLASTN is related to: genBlastA has parent organization: NCBI is required by: RelocaTE works with: Whole Genome Shotgun (WGS) Project works with: BLASTClust works with: MOLE-BLAST works with: Genotyping |
National Library of Medicine | PMID:16845079 PMID:18440982 |
Free, Freely available, Tutorial available | OMICS_01436, nlx_84530, biotools:blast | http://blast.ncbi.nlm.nih.gov, https://bio.tools/blast, https://sources.debian.org/src/ncbi-blast+/ | SCR_004870 | NCBI Basic Local Alignment Search Tool, NCBI BLAST, Basic Local Alignment Search Tool, BLAST | 2026-09-12 12:56:18 | 17718 | ||||
|
miRNAKey Resource Report Resource Website 1+ mentions |
miRNAKey (RRID:SCR_004813) | miRNAKey | software resource | A software pipeline for the analysis of microRNA Deep Sequencing data. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:20801911 | OMICS_00364, biotools:mirnakey | https://bio.tools/mirnakey | SCR_004813 | 2026-09-12 12:56:17 | 6 | |||||||
|
SVMerge Resource Report Resource Website 10+ mentions |
SVMerge (RRID:SCR_004777) | SVMerge | software resource | Software pipeline to detect structural variants (SVs) by integrating calls from several existing SV callers, which are then validated and the breakpoints refined using local de novo assembly. The output is in BED format allowing for easy downstream analysis or viewing in a genome browser. It is modular and extensible allowing new callers to be incorporated as they become available. | structural variant, breakpoint, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
PMID:21194472 | biotools:svmerge, OMICS_00325 | https://bio.tools/svmerge | SCR_004777 | SVMerge - Enhanced structural variant and breakpoint detection | 2026-09-12 12:56:16 | 19 | ||||||
|
SVseq Resource Report Resource Website 1+ mentions |
SVseq (RRID:SCR_004804) | SVseq | software resource | Software for accurate and efficient calling of structural variations with low-coverage sequence data. Version 2 uses the BAM files of paired Illumina reads with soft-clip signature as input. It calls both deletions and insertions. | structural variant, deletion, insertion, breakpoint, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University of Connecticut; Connecticut; USA |
PMID:22537045 | OMICS_00327, biotools:svseq | https://bio.tools/svseq | SCR_004804 | SVseq2, SVseq1 | 2026-09-12 12:56:17 | 3 | ||||||
|
Minia Resource Report Resource Website 50+ mentions |
Minia (RRID:SCR_004986) | Minia | software resource | A short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
DOI:10.1186/1748-7188-8-22 | biotools:minia, OMICS_00022 | https://bio.tools/minia, https://sources.debian.org/src/minia/ | SCR_004986 | 2026-09-12 12:56:19 | 66 | |||||||
|
SMART Resource Report Resource Website 5000+ mentions |
SMART (RRID:SCR_005026) | SMART | analysis service resource, data access protocol, data analysis service, data or information resource, database, production service resource, service resource, software resource, web service | Software tool for identification and annotation of genetically mobile domains and analysis of domain architectures. | extracellular, gene, genetic, genetically, genome, architecture, chromatin, domain, mobile, phyletic, protein, proteome, signaling, structure, taxonomic, tertiary, bio.tools, FASEB list |
is used by: Mutation Annotation and Genomic Interpretation is listed by: bio.tools is listed by: Debian is related to: Eukaryotic Linear Motif is related to: Conserved Domain Database is related to: GOTaxExplorer has parent organization: EMBL - Bork Group |
European Union | PMID:18978020 PMID:16381859 PMID:14681379 PMID:10592234 PMID:9847187 PMID:9600884 |
Free, Freely available | nif-0000-03471, biotools:smart | http://smart.embl-heidelberg.de/, https://bio.tools/smart | SCR_005026 | Simple Modular Architecture Research Tool | 2026-09-12 12:56:19 | 8432 | ||||
|
MIP Scaffolder Resource Report Resource Website 1+ mentions |
MIP Scaffolder (RRID:SCR_005072) | MIP Scaffolder | software resource | A software program for scaffolding contigs produced by fragment assemblers using mate pair data such as those generated by ABI SOLiD or Illumina Genome Analyzer. | scaffolding, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Helsinki; Helsinki; Finland |
OMICS_00044, biotools:mip_scaffolder | https://bio.tools/mip_scaffolder | SCR_005072 | 2026-09-12 12:56:20 | 1 | ||||||||
|
T-lex Resource Report Resource Website 1+ mentions |
T-lex (RRID:SCR_005134) | T-lex | software resource | Software package for fast and accurate discovery, annotation, re-annotation and population analysis of Transposable Elements using Next-Generation Sequencing data. | transposable element, next-generation sequencing, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Stanford University; Stanford; California has parent organization: SourceForge |
GNU General Public License | biotools:t-lex2, OMICS_00121 | https://bio.tools/t-lex2 | SCR_005134 | T-lex package | 2026-09-12 12:56:21 | 4 | ||||||
|
ERANGE Resource Report Resource Website 10+ mentions |
ERANGE (RRID:SCR_005240) | ERANGE | software resource | Software for Mapping and Quantifying Mammalian Transcriptomes by RNA-Seq. Its functions are to (i) assign reads that map uniquely in the genome to their site of origin and, for reads that match equally well to several sites (''multireads''), assign them to their most likely site(s) of origin; (ii) detect splice-crossing reads and assign them to their gene of origin; (iii) organize reads that cluster together, but do not map to an already known exon, into candidate exons or parts of exons; and (iv) calculate the prevalence of transcripts from each known or newly proposed RNA, based on normalized counts of unique reads, spliced reads and multireads. The new candidate RNA regions produced can be thought of as ESTs, and, like ESTs, some are provisionally appended to existing gene models if they meet several additional criteria. Remaining unassigned candidate transcribed regions (labeled RNAFAR features) can then be used in conjunction with other confirming data to develop new or revised gene models. | transcriptome, rna-seq, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:18516045 | OMICS_01274, biotools:erange | https://bio.tools/erange | SCR_005240 | Enhanced Read Analysis of Gene Expression | 2026-09-12 12:56:23 | 30 | ||||||
|
RNA-SeQC Resource Report Resource Website 100+ mentions |
RNA-SeQC (RRID:SCR_005120) | RNA-SeQC | software resource | Java software which computes a series of quality control metrics for RNA-seq data and can compare sequencing quality across different samples or experiments to evaluate different experimental parameters. The input can be one or more BAM files, and the output consists of HTML reports and tab delimited files of metrics data. | java, bam file, html, sequence comparison, rnaseq, rna sequence, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Broad Institute |
PMID:22539670 | Acknowledgement requested, Public | biotools:rna-seqc, OMICS_01234 | https://bio.tools/rna-seqc | SCR_005120 | 2026-09-12 12:56:21 | 214 | ||||||
|
READSCAN Resource Report Resource Website 1+ mentions |
READSCAN (RRID:SCR_005204) | READSCAN | software resource | A highly scalable parallel software program to identify non-host sequences (of potential pathogen origin) and estimate their genome relative abundance in high-throughput sequence datasets. | pathgen, genome, sequence, high-throughput sequence, align, read, host, microbe, virus, taxon, simulation, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: King Abdullah University of Science and Technology; Makkah Province; Saudi Arabia |
PMID:23193222 | OMICS_00222, biotools:readscan | https://bio.tools/readscan | SCR_005204 | 2026-09-12 12:56:22 | 5 | |||||||
|
VirusSeq Resource Report Resource Website 10+ mentions |
VirusSeq (RRID:SCR_005206) | VirusSeq | software resource | An algorithmic software tool for detecting known viruses and their integration sites using next-generation sequencing of human cancer tissue. VirusSeq takes FASTQ files (paired-end reads) as input. | next-generation sequencing, virus, integration site, cancer tissue, genome, rna-seq, whole genome sequencing, fastq, paired-end read, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Texas MD Anderson Cancer Center |
Cancer | OMICS_00227, biotools:virusseq | https://bio.tools/virusseq | SCR_005206 | 2026-09-12 12:56:22 | 23 | |||||||
|
MethPipe Resource Report Resource Website 100+ mentions |
MethPipe (RRID:SCR_005168) | MethPipe | software resource | A computational pipeline for analyzing bisulfite sequencing data. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University of Southern California; Los Angeles; USA |
PMID:24324667 | biotools:methpipe, OMICS_00603 | https://bio.tools/methpipe | SCR_005168 | 2026-09-12 12:56:22 | 108 | |||||||
|
SnpEff Resource Report Resource Website 5000+ mentions |
SnpEff (RRID:SCR_005191) | SnpEff | software resource | Genetic variant annotation and effect prediction software toolbox that annotates and predicts effects of variants on genes (such as amino acid changes). By using standards, such as VCF, SnpEff makes it easy to integrate with other programs. | genome, genetic variant, annotation, effect, variant, gene, cancer variant, gatk, hgsv, single nucleotide polymorphisms, genome sequence, java, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: Galaxy is related to: GATK has parent organization: SourceForge has parent organization: Wayne State University; Michigan; USA works with: SnpSift |
Cancer | PMID:22728672 | Free, Freely available | biotools:snpeff, OMICS_00186 | https://bio.tools/snpeff, https://sources.debian.org/src/snpeff/ | SCR_005191 | SnpEff - Genetic variant annotation and effect prediction toolbox | 2026-09-12 12:56:22 | 5640 | ||||
|
SimRare Resource Report Resource Website 1+ mentions |
SimRare (RRID:SCR_005226) | SimRare | software resource | A stand-alone executable software with user-friendly graphical interface implemented in Python/C++ for rare variant association studies. It is designed as a unified simulation framework to provide an unbiased and easy manner to evaluate association methods, including novel methods, under a broad range of choice of biological contexts. It consists of three modules, variant data simulator, genotype/phenotype generator and association method evaluator. SimRare generates variant data for gene regions using forward-time simulation which incorporates realistic population demographic and evolutionary scenarios. For phenotype data it is capable of generating both case-control and quantitative traits. The phenotypic effects of variants can be detrimental, protective or non-causal. SimRare has a graphical user interface which allows for easy entry of genetic and phenotypic parameters. Simulated data can be written into external files in a standard format. For novel association method implemented in R it can be imported into SimRare, which has been equipped built in functions to evaluate performance of new method and visually compare it with currently available ones in an unbiased manner. | statistical genetics, simulation framework, gui, association test, sequencing, rare variant, python, c++, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Google Code has parent organization: Baylor University; Texas; USA |
PMID:22914216 | Acknowledgement requested, GNU General Public License, v3 | OMICS_00257, biotools:simrare | https://bio.tools/simrare | SCR_005226 | SimRare - A program to generate and analyze sequence-based data for rare variant association studies of quantitative and qualitative traits | 2026-09-12 12:56:23 | 2 | |||||
|
PHAge Search Tool Resource Report Resource Website 100+ mentions |
PHAge Search Tool (RRID:SCR_005184) | PHAST | analysis service resource, data analysis service, data or information resource, data set, production service resource, service resource | A web server designed to rapidly and accurately identify, annotate and graphically display prophage sequences within bacterial genomes or plasmids. It accepts either raw DNA sequence data or partially annotated GenBank formatted data and rapidly performs a number of database comparisons as well as phage cornerstone feature identification steps to locate, annotate and display prophage sequences and prophage features. Relative to other prophage identification tools, PHAST is up to 40 times faster and up to 15% more sensitive. It is also able to process and annotate both raw DNA sequence data and Genbank files, provide richly annotated tables on prophage features and prophage quality and distinguish between intact and incomplete prophage. PHAST also generates downloadable, high quality, interactive graphics that display all identified prophage components in both circular and linear genomic views. Databases available for download include Virus DB, Prophage and virus DB, Bacteria DB, and PHAST result DB. Pre-calculated genomes for viewing are also available. | prophage sequence, genome, prophage, sequence, bacterial genome, plasmid, dna sequence, graph, phage, annotate, virus, nucleotide sequence, fasta, annotated genome, genbank, bio.tools, FASEB list |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University of Alberta; Alberta; Canada |
PMID:21672955 | Acknowledgement requested | biotools:phast, OMICS_00180 | https://bio.tools/phast | SCR_005184 | PHAST - PHAge Search Tool | 2026-09-12 12:56:22 | 243 | |||||
|
Breakpointer Resource Report Resource Website 10+ mentions |
Breakpointer (RRID:SCR_005254) | Breakpointer | software resource | A fast tool for locating sequence breakpoints from the alignment of single end reads (SE) produced by next generation sequencing (NGS). It adopts a heuristic method in searching for local mapping signatures created by insertion/deletions (indels) or more complex structural variants(SVs). With current NGS single-end sequencing data, the output regions by Breakpoint mainly contain the approximate breakpoints of indels and a limited number of large SVs. Notably, Breakpointer can uncover breakpoints of insertions which are longer than the read length. Breakpointer also can find breakpoints of many variants located in repetitive regions. The regions can be used not only as a extra support for SV predictions by other tools (such as by split-read method), but also can serve as a database for searching variants which might be missed by other tools. Breakpointer is a command line tool that runs under linux system. Breakpointer takes advanage of two local mapping features of single-end reads as a consequence of indel/SVs: 1) non-uniform read distribution (depth skewness) and 2) misalignments at the boundaries of indel/SVs. These features are summarized as breakpoint signature. Breakpointer proceeds in three stages in capturing this signature. It is implemented in C++ and perl. Input is the file or files containing alignments of single-end reads against a reference genome (in .BAM format). Output is the predicted regions containing potential breakpoints of SVs (in .GFF format). To be able to read in .BAM files, Breakpointer requires bamtools API, which users should install beforehand. | next-generation sequencing, c++, perl, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Max Planck Institute for Molecular Genetics; Berlin; Germany |
GNU General Public License | biotools:breakpointer, OMICS_00308 | https://bio.tools/breakpointer | SCR_005254 | 2026-09-12 12:56:23 | 10 | |||||||
|
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 | 2026-09-12 12:56:23 | 1 | |||||||
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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 | 2026-09-12 12:56:23 | 29 |
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