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GATK / Genome Analysis ToolKit

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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 an assortment of command line allowing one to analyze of high-throughput sequencing (HTS) data in various formats such as SAM, BAM, CRAM or VCF. The website includes multiple documentation for guiding users.


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Allows users to interact with high-throughput sequencing data. SAMtools permits the manipulation of alignments in the SAM/BAM/CRAM formats: reading, writing, editing, indexing, viewing and converting SAM/BAM/CRAM format. It limits the mapping quality of reads with excessive mismatches and applies base alignment quality to fix alignment errors. This tool can sort and merge alignments, remove polymerase chain reaction (PCR) duplicates or generate per-position information.


Examines epigenomic and transcriptomic next generation sequencing (NGS) data. Octopus-toolkit can be used for antibody- or enzyme-mediated experiments and studies for the quantification of gene expression. It can accelerate the data mining of public epigenomic and transcriptomic NGS data for basic biomedical research. This tool provides a private and a public mode: one to process the user’s own data, and the other to analyze public NGS data by retrieving raw files from the GEO database.


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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 manner, (2) variant calling using the Genome Analysis Toolkit (GATK) and (3) vigorous filtering of false-positive calls. The software allows the detection of variants even for lowly expressed genes. It was applied to data from the GM12878 human lymphoblastoid cell line and peripheral blood mononuclear cells (PBMCs) from another healthy individual.


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 realignment, built-in capability of de-duplication, detection of polymerase chain reaction (PCR) artifacts, accepting both DNA- and RNA-seq, paired analysis to detect variant frequency shifts alongside somatic and loss of heterozygosity (LOH) variant detection and structural variant (SV) calling. VarDict facilitates application of next-generation sequencing in cancer research, enabling researchers to use one tool in place of an alternative computationally expensive ensemble of tools.


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 previously identified single nucleotide polymorphism (SNP) map databases, and without data from separate individuals. By using only single RNA-seq libraries from a small number of pooled mutant individuals and their phenotypically wild-type siblings, it requires few animals and less sequencing data than required for whole-genome sequence mapping.

TRAPLINE / Transparent Reproducible and Automated PipeLINE

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 protein-protein interactions (PPIs), miRNA targets and alternatively splicing variants or promoter enriched sites. This tool includes different modules for several functions: (1) it scans the list of differentially expressed genes; (2) it includes modules for miRNA target prediction; and (3) a module is implemented to identify verified interactions between proteins of significantly upregulated and downregulated mRNAs.

aRNApipe / automated RNA-seq pipeline

Analyzes single-end and stranded or unstranded paired-end RNA-seq data. aRNApipe focuses on high performance computing (HPC) environments and the independent designation of computational resources at each stage allowing optimization of HPC resources. It is highly flexible because its project configuration and management options. This tool can be adapted to changes in the current applications and the addition of new functionalities. It allows users to complete primary RNA-seq analysis.

TWAS / Transcriptome-Wide Association Study

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. the modalities of the phenotype) with at least two replicates each, and outputs variants associated with the condition. The method does not require any reference genome, nor a database of SNPs. TWAS can therefore be applied to any species for a very reasonable cost.

BPS / BreakPoint Surveyor

Examines breakpoint predictions, together with their associated structural variation and gene context. BPS is a pipeline for integrating large, complex data sets with a scalable architecture supporting analysis from individual samples on a laptop to very large data sets on compute clusters. Its rendering engine is coupled with a flexible pipeline to detect structural variants, and it accommodates a variety of toolsets and analyses of whole genome sequencing (WGS) and RNA sequencing (RNA-Seq) data.


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 RNA-seq assays as input :(i) the first class involves Poisson, Binomial and Negative Binomial models, which explicitly model digital gene expression as a function of genetic variation and (ii) the second class involves a Normal/Gaussian model, which relies on appropriate transformations of gene expression data.


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 manage and exploit SNPs derived from next generation sequencing technologies, such as GBS (genotyping by sequencing), WGRS (whole gre-sequencing) and RNA-Seq technologies. Based on the standard VCF (variant call format) format, the application offers an intuitive interface for filtering and comparing polymorphisms using user-defined sets of individuals and then establishing a reliable genotyping data matrix for further analyses. Namely, in addition to the various scaled-up analyses allowed by the application (genomic annotation of SNP, diversity analysis, haplotype reconstruction and network, linkage disequilibrium), SNiPlay3 proposes new modules for GWAS (genome-wide association studies), population stratification, distance tree analysis and visualization of SNP density.


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 GATK-based pipeline for calling single nucleotide variants (SNVs) including single nucleotide polymorphisms (SNPs) and RNA editing events in RNA-seq reads, with our rigorous rMATS statistical model for identifying differential isoform ratios using RNA-seq sequence count data with replicates.


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 been mapped in different chromosomes. Opossum also discards duplicate reads based on the start and end positions of the read pair. Furthermore, it merges overlapping paired-end reads. The software has been designed to work specifically with Platypus, but it can be used equally well with other variant callers such as GATK.


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, core-workflow, post-mapping and sequence variation detection. It also turns the identification of fusion genes, single nucleotide polymorphisms (SNP), long noncoding RNAs and circular RNAs. Finally, this pipeline is specifically designed for performing the systematic analysis on a huge set of samples in one go, ideally for the researchers who intend to deploy the pipeline on their local servers.

VaDiR / Variant Detection in RNA

Assists users in detecting variations in coding and non-coding sequences. VaDiR is a program that supplies methodology to uncover mutations from RNA sequencing datasets. It also allows orthogonal validation of DNA-based mutation discovery by providing complementary sequence variation analysis from paired RNA/DNA sequencing data sets. This program can be used for the comparison of somatic variants in high-grade serous carcinomas collected from patients with chemotherapy-resistant or sensitive ovarian cancer.


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 concordant and discordant RNA-seq read alignments. It can detect both fusion-gene events and TSVs incorporating previously non-transcribed regions into transcripts. Using an integer linear program rearranges the segments of the reference genome so that as many read alignments as possible are concordant with the rearranged sequence.


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 module allows to align and filter out human RNA sequences; the second module maps and count (remaining un-aligned) reads against reference genomes of all known and sequenced human viruses; the third module quantifies read counts at the individual viral genes level thus allowing for downstream differential expression analysis of viral genes between experimental and controls groups, and the fourth module calls variants in these viruses.


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 Genotyper from GATK for raw variant calling in the target region and generation of the annotations including all GATK classic annotations, annotation of each variant with additional attributes, variant prioritization and ranking using a novel boosting method to train the variant classifying model using high-confidence variants, and ranking of the likelytrue variants using a confidence score.

Array Studio

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) differs from standard desktop solutions or open source solutions, with Array Studio providing the graphical user interface for NGS and omic analysis and visualization and Array Server providing the enterprise back-end solution for project management, sample management and data storage.