Services: Software Tools

Based on ICGC PanCancer infrastructure for organising and processing NGS data using workflow plugins including:  

• Workflow Plug-Ins - provide pipelines for the most common NGS processing tasks, including alignment (WES, WGS, WGBS, RNA-seq), quality control and variant calling (SNV, indel, CNV, SV).
• Cloud/HPC - IT Infrastructure for de.NBI users based on ICGC and TCGA PanCancer technology
• OTP - "One Touch Pipeline" is a comprehensive framework for NGS project organization and processing.
• Roddy - a framework for large scale NGS processing pipelines on Petabyte scale for the management of workflows in the Pan-Cancer Analysis of Whole Genomes (PCAWG) project.

The OpenMS Proteomics Pipeline making a range of tools available, including MetaProSIP and TOPPview. 

Visualising own data through OpenMS tools, including spectra, chromatograms, 2D LC-MS data and annotations. 

Template-based RNA secondary structure visualization.

A multiple sequence alignment package that can be used for DNA, RNA and protein sequences. It can be used to align sequences or to combine the output of other alignment methods (Clustal, Mafft, Probcons, Muscle...) into one unique alignment.

Trimmomatic is a flexible read trimming tool for NGS data.

Platform for metaproteomics data analysis with a focus on interactive data visualizations

UniProt Related Documents (UniReD): assisting wet lab biologists
in their quest on finding novel counterparts in a protein network

Tools for processing the topology and structure of transmembrane proteins

• A. Constrained Consensus TOPology prediction server (CCTOP) 
• B. Transmembrane helices and protein topology prediction (HMMTOP),
• C. Detection of transmembrane regions (TMDET)
• D. Transmembrane proteins’ membrane segments folding recognizing (TmFoldWeb)

Public Galaxy instance enabling reproducible data analysis through workflows

V-pipe is the bioinformatics pipeline that integrates various open-source software packages for assessing viral genetic diversity from next-generation sequencing (NGS) data derived from intra-host virus populations. V-pipe enables reliable and comparable viral pathogen genomics and epidemiological studies and facilitates clinical diagnostics of viruses.

VarAFT is a software designed to annotate and filter Human NGS data. This system was developed within the RD-Connect project and was instrumental for the creation of the RD-Connect Genome-Phenome platform. As a stand-alone java system, it ensures full data protection, critical for clinical use. VarAFT provides experiments’ quality, annotates, and allows the filtration of VCF files. Data from multiple samples can be combined to address different Mendelian Inherited Disorders, Population Genetics or Cancers. It contains unique variant priorization features including OMIM, HPO, Gene Ontology, pathways and predictions from UMD-Predictor and Human Splicing Finder in addition to classical annotations from dbNSFP . It is used by many research and clinical laboratories worldwide.

Performs ranking of variants in genomic datasets, integrating information from multiple sources to prioritize each variant by its deleteriousness, novelty and existing information.

Accurate validation, mapping and formatting of sequence variant descriptions

A high recall search engine to support the curation of genomic variants.

https://academic.oup.com/bioinformatics/article/38/9/2595/6547047

Galaxy server for the functional annotation and prioritization of genetic variants.

WarPP is a fully automated procedure to place water molecules in the active site of a protein structure. 

A web-accessible, single cell RNA-Seq processing platform designed for the management, analysis and interpretation of scRNA-seq high-throughput data.

A software package for the automatic discovery of enriched motifs in a set of related DNA sequences, including ChIP-Seq peaks.

WESkit is an open source implementation of a Workflow Execution Service (WES). It tries to be GA4GH-compliant.

WheatIS is a portal that enables data discovery through an international federation of distant informations systems about wheat genetics and genomics in the frame of the Wheat Initiative (www.wheatinitiative.org). The WheatIS portal allows a keyword-based discovery of any type of data. It currently gives a single entry point to data provided by twelve different worldwide institutes.

Federated genomics data sharing platform allowing users to query genomic and phenotypic information.

Workflow Execution Service automating a number of steps, including: 

1. Fetch and cache a workflow a number of sources
2. Identify the kind of workflow.
3. Fetch and set up workflow execution engine
4. Identify the needed containers by the workflow
5. Execute the workflow in a secure way

Workflow plugins provide pipelines for the most common NGS processing tasks, including alignment (WES, WGS, WGBS, RNA-seq), quality control and variant calling (SNV, indel, CNV, SV).

Workflow plugins provide pipelines for the most common NGS processing tasks, including alignment (WES, WGS, WGBS, RNA-seq), quality control and variant calling (SNV, indel, CNV, SV).

Workflow4Metabolomics resource is based on the Galaxy environment that provides user-friendly interfaces to build, run, and share comprehensive data analysis workflows and gives access to a High Performance Computing environment the ELIXIR-FR/IFB infrastructure. Thus, W4M offers more than 40 tools to process data from all three main technologies (NMR, GCMS, LCMS), including unique algorithms developed by the W4M developers themselves. Data and workflows can be re-used and publicly shared, thus becoming useful references for the community. Finally, the platform provides many tutorials and a help desk.

This package provides functions and routines for a supervised analysis of somatic signatures. In particular, functions to perform a signature analysis with known signatures (LCD = linear combination decomposition) and a signature analysis on stratified mutational catalogue (SMC = stratify mutational catalogue) are provided.

Repository of regulatory associations between transcription factors and target genes in Saccharomyces cerevisiae.