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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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University of Iowa Carver College of Medicine; Iowa; USA Resource Report Resource Website 1+ mentions |
University of Iowa Carver College of Medicine; Iowa; USA (RRID:SCR_005064) | UI Carver College of Medicine | university | Medical school of the University of Iowa, located in Iowa City, in the U.S. state of Iowa. |
has parent organization: University of Iowa; Iowa; USA is parent organization of: MADS+ - discovery of differential splicing events from Affymetrix exon junction array data is parent organization of: University of Iowa College of Medicine Department of Pharmacology is parent organization of: University of Iowa Magnetic Resonance Research Facility is parent organization of: University of Iowa Center for Gene Therapy Vectore Core is parent organization of: University of Iowa Center for Gene Therapy Clinical Core is parent organization of: University of Iowa Center for Gene Therapy Animal Model Core is parent organization of: University of Iowa Center for Gene Therapy is parent organization of: University of Iowa Center for Gene Therapy Comparative Pathology Core is parent organization of: University of Iowa Center for Gene Therapy Cell Tissue Core |
nlx_68753 | SCR_005064 | University of Iowa Carver College of Medicine, Roy J. and Lucille A. Carver College of Medicine | 2026-07-25 12:05:58 | 1 | |||||||||
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G-BLASTN Resource Report Resource Website |
G-BLASTN (RRID:SCR_005062) | G-BLASTN | software resource | A GPU-accelerated nucleotide alignment tool based on the widely used NCBI-BLAST. It can produce exactly the same results as NCBI-BLAST, and it also has very similar user commands. It also supports a pipeline mode, which can fully utilize the GPU and CPU resources when handling a batch of medium to large sized queries. | parallel computation 4, blast, alignment, nucleotide, gpu, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: NCBI BLAST has parent organization: Hong Kong Baptist University; Hong Kong; China has parent organization: SourceForge |
Hong Kong Baptist University; Hong Kong; China FRG2/11-12/158; NVIDIA |
PMID:24463183 | Free | OMICS_02263, biotools:g-blastn | http://sourceforge.net/projects/gblastn/, https://bio.tools/g-blastn | SCR_005062 | 2026-07-25 12:06:00 | 0 | |||||
|
SLIDE Resource Report Resource Website 10+ mentions |
SLIDE (RRID:SCR_005137) | SLIDE | software resource | Software package that takes exon boundaries and RNA-Seq data as input to discern the set of mRNA isoforms that are most likely to present in an RNA-Seq sample. It is based on a linear model with a design matrix that models the sampling probability of RNA-Seq reads from different mRNA isoforms. To tackle the model unidentifiability issue, SLIDE uses a modified Lasso procedure for parameter estimation. Compared with deterministic isoform assembly algorithms (e.g., Cufflinks), SLIDE considers the stochastic aspects of RNA-Seq reads in exons from different isoforms and thus has increased power in detecting more novel isoforms. Another advantage of SLIDE is its flexibility of incorporating other transcriptomic data such as RACE, CAGE, and EST into its model to further increase isoform discovery accuracy. SLIDE can also work downstream of other RNA-Seq assembly algorithms to integrate newly discovered genes and exons. Besides isoform discovery, SLIDE sequentially uses the same linear model to estimate the abundance of discovered isoforms. |
is listed by: OMICtools has parent organization: University of California at Berkeley; Berkeley; USA |
NIH ; NHGRI HG004695; NHGRI HG005639; NEI EY019094 |
PMID:22135461 | OMICS_01291 | SCR_005137 | sparse linear modeling of RNA-Seq data for isoform discovery and abundance estimation | 2026-07-25 12:05:59 | 32 | |||||||
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VFS Resource Report Resource Website 1+ mentions |
VFS (RRID:SCR_005138) | VFS | software resource | A versatile high-throughput sequencing (HTS) tool for discovering viral integration events and reconstruct fusion transcripts at single-base resolution. It combines soft-clipping information, read-pair analysis, and targeted de novo assembly to discover and annotate viral-human fusion events. A simple yet effective empirical statistical model is used to evaluate the quality of fusion breakpoints. Minimal user defined parameters are required. | ubuntu, debian, high-throughput sequencing, virus, reconstruct, fusion transcript, transcript, integration, fusion, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge has parent organization: Chinese University of Hong Kong; Hong Kong; China |
PMID:23314323 | GNU General Public License, v3 | OMICS_00224, biotools:viralfusionseq | https://bio.tools/viralfusionseq | SCR_005138 | ViralFusionSeq, ViralFusionSeq (VFS) | 2026-07-25 12:06:00 | 1 | |||||
|
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 | 2026-07-25 12:06:00 | 45 | |||||||
|
Cloudbreak Resource Report Resource Website |
Cloudbreak (RRID:SCR_005097) | software resource | Software providing a Hadoop-based genomic structural variation (SV) caller for Illumina paired-end DNA sequencing data. It contains a full pipeline for aligning data in the form of FASTQ files using alignment pipelines that generate many possible mappings for every read, in the Hadoop framework. It then contains Hadoop jobs for computing genomic features from the alignments, and for calling insertion and deletion variants from those features. | illumina, mapreduce, insertion, deletion, genomic | is listed by: OMICtools | OMICS_04078 | SCR_005097 | 2026-07-25 12:05:58 | 0 | ||||||||||
|
MMAPPR Resource Report Resource Website 1+ mentions |
MMAPPR (RRID:SCR_005092) | MMAPPR | software resource | A software analysis pipeline for mapping mutations using RNA-seq that works without parental strain information, without the requirement of a pre-existing snp map of the organism, and without erroneous assumptions that recombination occurs at the same frequency across the genome. In addition, it compensates for the considerable amount of noise in RNA-seq datasets and simultaneously identifies the region where the mutation lies and generates a list of putative coding region mutations in the linked genomic segment. MMAPPR can utilize RNA-seq datasets from isolated tissues or whole organisms that are often generated for phenotypic analysis and gene network analysis in novel mutants. | mutation, rna-seq, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Utah; Utah; USA |
PMID:23299975 | Acknowledgement requested | OMICS_01361, biotools:mmappr | https://bio.tools/mmappr | SCR_005092 | Mutation Mapping Analysis Pipeline for Pooled RNA-seq | 2026-07-25 12:06:01 | 7 | |||||
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MJ Murdock Charitable Trust Resource Report Resource Website 1+ mentions |
MJ Murdock Charitable Trust (RRID:SCR_005122) | Murdock Trust | institution | The M. J. Murdock Charitable Trust seeks to enrich the quality of life in the Pacific Northwest by providing grants and enrichment programs to non-profit organizations that seek to strengthen the region''s educational, spiritual, and cultural base in creative and sustainable ways. In addition to a special interest in education and scientific research, the Trust partners with a wide variety of organizations that serve the arts, public affairs, health and medicine, human services, leadership development, and persons with disabilities. Eligibility for scientific research grants is limited. Select public research universities and medical institutes located within the five-state region (Pacific Northwest: Alaska, Washington, Oregon, Idaho, Montana) are typically considered for funding. The Trust prefers requests for projects in the natural sciences where the main objective is the acquisition of new knowledge. However, requests for research in engineering and medicine are also eligible. Training students in conducting research is an important consideration. | grant, enrichment program, life science, research, natural science | grid.453269.f, Crossref funder ID: 100000937, nlx_144130 | https://ror.org/02hxgd925 | SCR_005122 | Murdock Charitable Trust, Murdock Trust | 2026-07-25 12:05:59 | 8 | ||||||||
|
FusionMap Resource Report Resource Website 50+ mentions |
FusionMap (RRID:SCR_005242) | FusionMap | software resource | An efficient fusion aligner which aligns reads spanning fusion junctions directly to the genome without prior knowledge of potential fusion regions. It detects and characterizes fusion junctions at base-pair resolution. FusionMap can be applied to detect fusion junctions in both single- and paired-end dataset from either gDNA-Seq or RNA-Seq studies. FusionMap runs under both Windows and Linux (requiring MONO) environments. Although it can run on 32 bit machine, it is recommended to run on 64-bit machine with 8GB RAM or more. If you have an ArrayStudio License, you can run the fusion detection easily through its GUI. | windows, linux, c#, fusion gene, next-generation sequencing, gene, reference indexing, read filtering, fusion alignment, reporting, alignment, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:21593131 | Free, Non-commercial | biotools:fusionmap, OMICS_00316 | https://bio.tools/fusionmap | SCR_005242 | 2026-07-25 12:06:00 | 88 | ||||||
|
Traph Resource Report Resource Website 1+ mentions |
Traph (RRID:SCR_005119) | Traph | software resource | A software tool for transcript identification and quantification with RNA-Seq. The method has a two-fold advantage: on the one hand, it translates the problem as an established one in the field of network flows, which can be solved in polynomial time, with different existing solvers; on the other hand, it is general enough to encompass many of the previous proposals under the least sum of squares model. |
is listed by: OMICtools has parent organization: University of Helsinki; Helsinki; Finland |
PMID:23734627 | Acknowledgement requested | OMICS_01295 | SCR_005119 | Transcripts in gRAPHs - Traph: A tool for transcript identification and quantification with RNA-Seq, Transcripts in gRAPHs | 2026-07-25 12:06:02 | 3 | |||||||
|
rQuant Resource Report Resource Website 1+ mentions |
rQuant (RRID:SCR_005150) | rQuant | software resource | Software for quantitative detection of alternative transcripts with RNA-Seq data. The method, based on quadratic programming, estimates biases introduced by experimental settings and is thus a powerful tool to reveal and quantify novel (alternative) transcripts. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: Galaxy |
PMID:20551130 | biotools:rquant.web, OMICS_01286 | https://bio.tools/rquant.web | SCR_005150 | rQuant: quantitative detection of alternative transcripts with RNA-Seq data | 2026-07-25 12:05:59 | 1 | ||||||
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University of Eastern Finland at Kuopio; Kuopio; Finland Resource Report Resource Website |
University of Eastern Finland at Kuopio; Kuopio; Finland (RRID:SCR_005214) | university | University of Eastern Finland was formed through merger of two formerly independent universities, the University of Joensuu and the University of Kuopio.Public University of Eastern Finland Kuopio Campus is located in the Savilahti area. |
is related to: AddNeuroMed is parent organization of: UKU Neuroscience and Neurology Links |
nlx_14711 | http://www.uku.fi/english/ | SCR_005214 | 2026-07-25 12:06:03 | 0 | ||||||||||
|
ShoRAH Resource Report Resource Website 10+ mentions |
ShoRAH (RRID:SCR_005211) | ShoRAH | software resource | A software package that allows for inference about the structure of a population from a set of short sequence reads as obtained from ultra-deep sequencing of a mixed sample. The package contains programs that support mapping of reads to a reference genome, correcting sequencing errors by locally clustering reads in small windows of the alignment, reconstructing a minimal set of global haplotypes that explain the reads, and estimating the frequencies of the inferred haplotypes. | linux, mac os x, windows, next-generation sequencing, c++, python, perl, structure, population, short sequence read, haplotype, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: ETH Zurich; Zurich; Switzerland |
PMID:21521499 | GNU General Public License, v3 | biotools:shorah, OMICS_00231 | https://bio.tools/shorah | SCR_005211 | Short Reads Assembly into Haplotypes, ShoRAH - Short Reads Assembly into Haplotypes | 2026-07-25 12:06:03 | 35 | |||||
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V-Phaser 2 Resource Report Resource Website 1+ mentions |
V-Phaser 2 (RRID:SCR_005212) | V-Phaser 2 | software resource | A software tool to call variants in genetically heterogeneous populations from ultra-deep sequence data. It combines information regarding the covariation (i.e. phasing) between observed variants to increase sensitivity and an expectation maximization algorithm that iteratively recalibrates base quality scores to increase specificity. V-Phaser can reliably detect rare variants in diverse populations that occur at frequencies of <1%. V-Phaser 2 is a complete rewrite of the original V-Phaser. It contains a new model for length polymorphisms (indels) and incorporates paired end read information in its phasing model. The data access and probability computation sections of the code have also been highly optimized, resulting in substantial improvements in running time and memory usage. | variant, polymorphism, indel, virus, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Broad Institute |
NIAID | PMID:24088188 | Free for academic use, Non-commercial, Http://www.broadinstitute.org/scientific-community/science/projects/viral-genomics/viral-genomics-software-license-v-phaser-2 | biotools:v-phaser, OMICS_00232 | https://bio.tools/v-phaser | SCR_005212 | 2026-07-25 12:06:00 | 2 | |||||
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NSMAP Resource Report Resource Website 1+ mentions |
NSMAP (RRID:SCR_005213) | NSMAP | software resource | Software designed to identify and quantify isoforms from RNA-seq by incorporating a sparsity term into expression level estimation to enable isoform structure prediction and expression estimation simultaneously. | is listed by: OMICtools | PMID:21575225 | Free, Public | OMICS_01282 | SCR_005213 | Nonnegativity and Sparsity constrained Maximum A Posteriori, NSMAP for RNA-seq, NSMAP: A Method for Spliced Isoforms Identification and Quantification from RNA-Seq | 2026-07-25 12:06:01 | 1 | |||||||
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COVA Resource Report Resource Website 50+ mentions |
COVA (RRID:SCR_005175) | COVA | software resource | A variant annotation and comparison tool for next-generation sequencing. It annotates the effects of variants on genes and compares those among multiple samples, which helps to pinpoint causal variation(s) relating to phenotype. | next-generation sequencing, variant annotation, variant, annotation, gene, genetic variation, phenotype |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00171 | SCR_005175 | COVA - Comparison of variants and functional annotation, Comparison of variants and functional annotation | 2026-07-25 12:05:59 | 58 | ||||||||
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PredictHaplo Resource Report Resource Website 10+ mentions |
PredictHaplo (RRID:SCR_005207) | PredictHaplo | software resource | Software for reconstructing haplotypes from next-generation sequencing data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | haplotype, next-generation sequencing |
is listed by: OMICtools has parent organization: University of Basel; Basel; Switzerland |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00228 | SCR_005207 | 2026-07-25 12:06:03 | 15 | ||||||||
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QuRe Resource Report Resource Website 1+ mentions |
QuRe (RRID:SCR_005209) | QuRe | software resource | A software program for viral quasispecies reconstruction, specifically developed to analyze long read (>100 bp) next-generation sequencing (NGS) data. The software performs alignments of sequence fragments against a reference genome, finds an optimal division of the genome into sliding windows based on coverage and diversity and attempts to reconstruct all the individual sequences of the viral quasispecies--along with their prevalence--using a heuristic algorithm, which matches multinomial distributions of distinct viral variants overlapping across the genome division. QuRe comes with a built-in Poisson error correction method and a post-reconstruction probabilistic clustering, both parameterized on given error rates in homopolymeric and non-homopolymeric regions. | next-generation sequencing, virus, long read, reconstruction |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00230 | SCR_005209 | qure - software for viral quasispecies reconstruction from next-gen seq. data | 2026-07-25 12:06:00 | 6 | ||||||||
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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 | 2026-07-25 12:06:00 | 16 | |||||||
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RNA-eXpress Resource Report Resource Website 1+ mentions |
RNA-eXpress (RRID:SCR_005167) | RNA-eXpress | software resource | Software designed as a user friendly solution to extract and annotate biologically important transcripts from next generation RNA sequencing data. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Monash University; Melbourne; Australia |
PMID:23396121 | Acknowledgement requested, Non-Profit | biotools:rna-express, OMICS_01285 | https://bio.tools/rna-express | SCR_005167 | 2026-07-25 12:05:59 | 5 |
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Data set from Kravitz, Owen and Kretizer's 2012 paper "Optogenetic identification of striatal projection neuron subtypes during in vivo recordings."
