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Variant detection software tools | RNA sequencing data analysis

Identifying genomic variation is a crucial step for unraveling the relationship between genotype and phenotype and can yield important insights into human diseases. Prevailing methods rely on cost-intensive whole-genome sequencing (WGS) or…
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SAMtools
Desktop

SAMtools

A suite of programs for interacting with high-throughput sequencing data. It…

A suite of programs for interacting with high-throughput sequencing data. It can manipulate alignments in the SAM/BAM/CRAM formats : reading, writing, editing, indexing, viewing and converting…

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GATK…
Desktop

GATK UnifiedGenotyper

A multiple-sample, technology-aware SNP and indel caller. It uses a Bayesian…

A multiple-sample, technology-aware SNP and indel caller. It uses a Bayesian genotype likelihood model to estimate simultaneously the most likely genotypes and allele frequency in a population of N…

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GATK
Desktop

GATK Genome Analysis ToolKit

Focuses on variant discovery and genotyping. GATK provides a toolkit, developed…

Focuses on variant discovery and genotyping. GATK provides a toolkit, developed at the Broad Institute, composed of several tools and ables to support projects of any size. The application compiles…

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VarDict
Desktop

VarDict

A versatile variant caller for both DNA- and RNA-sequencing data. VarDict…

A versatile variant caller for both DNA- and RNA-sequencing data. VarDict contains many features that are distinct from other variant callers, including linear performance to depth, intrinsic local…

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aRNApipe
Desktop

aRNApipe automated RNA-seq pipeline

Provides an integrated and efficient workflow for analyzing single-end and…

Provides an integrated and efficient workflow for analyzing single-end and stranded or unstranded paired-end RNA-seq data. Unlike previous pipelines, aRNApipe is focused on high performance computing…

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SNPiR
Desktop

SNPiR

Identifies single nucleotides polymorphisms (SNPs) in RNA-seq data. SNPiR…

Identifies single nucleotides polymorphisms (SNPs) in RNA-seq data. SNPiR consists of (1) a modified RNA-seq read-mapping procedure that allows alignment of reads to the reference in a splice-aware…

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MMAPPR
Desktop

MMAPPR

Maps mutations generated from forward genetic screens or that spontaneously…

Maps mutations generated from forward genetic screens or that spontaneously arise in a population. MMAPPR can identify candidate mutations without any parental strain or genotype information, without…

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CRAC
Desktop
Web

CRAC Complex Reads Analysis & Classification

An RNA-Seq mapping software tool that include the discovery of transcriptomic…

An RNA-Seq mapping software tool that include the discovery of transcriptomic and genomic variants like splice junction, chimeric junction, SNVs, Indels in a single analysis step using a built-in…

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TWAS
Desktop

TWAS Transcriptome-Wide Association Study

A method for the de novo identification, differential analysis and annotation…

A method for the de novo identification, differential analysis and annotation of variants from RNAseq data in non-model species. TWAS takes as input RNA-seq reads from at least two conditions (e.g.…

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QualitySNPng
Desktop

QualitySNPng

A software tool for the detection and visualisation of single nucleotide…

A software tool for the detection and visualisation of single nucleotide polymorphisms (SNPs) from next generation sequencing data that uses a haplotype-based strategy.

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QuasR
Desktop

QuasR

Provides an integrated analysis of high-throughput sequencing data in R,…

Provides an integrated analysis of high-throughput sequencing data in R, covering all steps from read preprocessing, alignment and quality control to quantification. QuasR supports different…

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TRAPLINE
Desktop

TRAPLINE Transparent Reproducible and Automated PipeLINE

Serves for RNAseq data processing, evaluation and prediction. TRAPLINE guides…

Serves for RNAseq data processing, evaluation and prediction. TRAPLINE guides researchers through the NGS data analysis process in a transparent and automated state-of-the-art pipeline. It can detect…

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hppRNA
Desktop

hppRNA

Converts the raw fastq files into gene/isoform expression matrix and…

Converts the raw fastq files into gene/isoform expression matrix and differentially expressed genes or isoforms. hppRNA is a one-in-all solution composed of four scenarios such as pre-mapping,…

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SePIA
Desktop

SePIA Sequence Processing Integration and Analysis

Automates RNA-seq processing, integration and analysis. SePIA allows…

Automates RNA-seq processing, integration and analysis. SePIA allows reproducible analysis of total RNA, poly(A)-derived RNA, small RNA, and integrated microRNA (miRNA) and mRNA data. It provides a…

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SNiPlay
Web

SNiPlay

A web-based tool for detection, management and analysis of genetic variants…

A web-based tool for detection, management and analysis of genetic variants including both single nucleotide polymorphisms (SNPs) and InDels. Version 3 now extends functionalities in order to easily…

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ACE
Web
Desktop

ACE

Detects resistance-associated mutations in ace genes from RNA-Seq data. ACE was…

Detects resistance-associated mutations in ace genes from RNA-Seq data. ACE was used to estimate the mutation frequencies in 7 important insect pests. It can detect resistant reads at low frequency…

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eSNV-detect
Desktop

eSNV-detect

A method to detect expressed single nucleotide variants (eSNVs) with high…

A method to detect expressed single nucleotide variants (eSNVs) with high specificity and sensitivity from the high throughput transcriptome sequencing data. Alignments from multiple aligners are…

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SQUID
Desktop

SQUID

Predicts transcriptomic structural variants (TSVs) from RNA-seq data. SQUID is…

Predicts transcriptomic structural variants (TSVs) from RNA-seq data. SQUID is a computational tool that divides the reference genome into segments and builds a genome segment graph from both…

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eQTLseq
Desktop

eQTLseq

Implements two classes of statistical models for detecting simultaneously…

Implements two classes of statistical models for detecting simultaneously multiple associations between gene expression and genomic polymorphisms in a population. eQTLseq uses paired DNA-seq and…

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rMATS-DVR
Desktop

rMATS-DVR

Streamlines the discovery of DVRs (Differential Variants in RNA) between two…

Streamlines the discovery of DVRs (Differential Variants in RNA) between two RNA-seq sample groups with replicates. rMATS-DVR is a convenient and user-friendly program to combines a stringent…

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Opossum
Desktop

Opossum

Performs several quality control measures such as discarding secondary…

Performs several quality control measures such as discarding secondary alignments, poorly mapped reads and read pairs where the two reads are pointing outwards or in the same direction, or that have…

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viGEN
Desktop

viGEN

Combines existing well-known and novel RNA-seq tools for not only detection and…

Combines existing well-known and novel RNA-seq tools for not only detection and quantification of viral RNA, but also variants in the viral transcripts. ViGEN includes 4 major modules: the first…

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PVAAS
Desktop

PVAAS Program to identify Variants Associated with Aberrant Splicing

A tool to identify single nucleotide variants that associated with aberrant…

A tool to identify single nucleotide variants that associated with aberrant alternative splicing from RNA-seq data. PVAAS works in 3 steps: 1) identify aberrant splicings; 2) use user provided…

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RNAmapper
Desktop
Web

RNAmapper

Uses RNA-seq data to identify both a region of the genome linked to a mutation…

Uses RNA-seq data to identify both a region of the genome linked to a mutation as well as candidate mutations that may be causal for the phenotype of interest. RNAmapper can identify mutations that…

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RVboost
Desktop

RVboost

A pipeline to prioritize RNA sequencing called variants using GATK framework…

A pipeline to prioritize RNA sequencing called variants using GATK framework (Genome Analysis Toolkit). RBboost gives a Q score to each variant seen in the data. It processes into 3 steps : Unified…

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RSVP
Desktop

RSVP

A software package for prediction of alternative isoforms of protein-coding…

A software package for prediction of alternative isoforms of protein-coding genes, based on both genomic DNA evidence and aligned RNA-seq reads.

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r-make
Desktop

r-make

A pipeline that processes RNA sequencing reads. r-make estimates the expression…

A pipeline that processes RNA sequencing reads. r-make estimates the expression levels for exons, genes, and splice junctions. In the process, it prints a range of quality metrics and statistics,…

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Torrent Suite…
Server

Torrent Suite Software

Provides a platform for handling various data analysis. Torrent Suite Software…

Provides a platform for handling various data analysis. Torrent Suite Software is composed of four mains modules that authorizes: (i) to create a run plan downloadable directly to the sequencer; (ii)…

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UltraFast…
Desktop

UltraFast Expressed Variant Calling

Identifies expressed variants from public databases such as NCBI SRA as well as…

Identifies expressed variants from public databases such as NCBI SRA as well as user’s own RNA-Seq data. UltraFast Expressed Variant Calling uses one of several RNA aligners and quantification…

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QRNAseq
Desktop

QRNAseq

A tool to manage huge amounts of RNA-seq data in an integrative way which…

A tool to manage huge amounts of RNA-seq data in an integrative way which includes RNA-seq data quality control, read alignment, gene fusion, gene mutation, isoform identification and function…

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Nesoni
Desktop

Nesoni

A high-throughput sequencing data analysis toolset. Nesoni focusses on…

A high-throughput sequencing data analysis toolset. Nesoni focusses on analysing the alignment of reads to a reference genome. Use of the SHRiMP and Bowtie2 read aligners is automated by nesoni. We…

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rnaseqmut
Desktop

rnaseqmut

An easy-to-use program to detect variants in RNA-Seq read alignments. rnaseqmut…

An easy-to-use program to detect variants in RNA-Seq read alignments. rnaseqmut is a light-weight C++ program to detect variants (or mutations, including SNPs, indels, RNA editing events) from a…

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Veridical
Desktop

Veridical

Variants predicted to alter mRNA splicing result are characterized by reads…

Variants predicted to alter mRNA splicing result are characterized by reads demonstrating exon skipping, cryptic splicing, or intron inclusion.Veridical automatically validation of DNA sequencing…

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NextGENe
Desktop

NextGENe

Software for Next Generation (NGS) Sequence Analysis.

Software for Next Generation (NGS) Sequence Analysis.

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Strand NGS
Desktop

Strand NGS

Provides analysis, management and visualization tools for next-generation…

Provides analysis, management and visualization tools for next-generation sequencing (NGS) data. Strand NGS supports extensive workflows for alignment, RNA-seq, small RNA-seq, DNA-seq, Methyl-seq,…

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Array Studio
Desktop

Array Studio

Provides the premier enterprise solution for data content, framework and…

Provides the premier enterprise solution for data content, framework and graphical user interface for omic and next-generation sequencing data analysis. Array Suite (Array Studio and Array Server)…

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ACCUSA
Desktop

ACCUSA

Identifies variant positions where nucleotide frequency spectra differ between…

Identifies variant positions where nucleotide frequency spectra differ between two samples. ACCUSA is a Single-Nucleotide Variant (SNV) calling software which integrates quality scores for base…

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