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Source: CDC / Alissa Eckert, MS; Dan Higgins, MAM / modified.
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The current coronavirus pandemic is a major challenge for our society and requires special attention through established scientific structures such as the de.NBI network. It is important to advance molecular biological research on coronaviruses, especially SARS-CoV-2, and to investigate both medical and epidemiological aspects of the infection process in COVID-19 disease. Bioinformatics tools from the de.NBI portfolio that can be applied to research on SARS-CoV-2 and COVID-19 are listed below. |
| Genome data analysis |
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| ACEseq | A computational tool for allele-specific copy number estimation in human genomes based on whole genome sequencing. |
| Alfred | BAM alignment statistics, feature counting and feature annotation. |
| DELLY | An integrated structural variant prediction method that can detect deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read sequencing data. |
| EDGAR | Performs genome comparisons in a high throughput approach. |
| Galaxy workflow for to analyse genomics and cheminformatics data related to COVID-19 | Best practices for the analysis of SARS-CoV-2 data: Genomics, Proteomics, Evolution, and Cheminformatics. |
| GEAR | A genome analysis web server hosting applications for molecular biologists to analyze Sanger traces, design PCR primers and perform DNA sequence analyses. GEAR has recently been expanded by the inclusion of SARS-CoV-2 sequences. |
| MapMyCorona | Compares SARS-CoV-2 sequences in order to display sequence similarity or alterations in a query sequence. MapMyCorona was recently developed especially for the coronavirus data analysis. |
| Magellan | A web application for the display and analysis of next-generation sequencing data. |
| MGX | A flexible and extensible client/server-framework for the management and analysis of metagenomic datasets. |
| OTP - One Touch Pipeline | A comprehensive framework for NGS project organization and processing. |
| Tools for exploring deep sequencing data | |
| Butler | An open-source framework that facilitates large-scale scientific data analysis on the cloud by providing a comprehensive toolkit for virtual infrastructure management. |
| deepTools | A suite of python tools developed for the efficient analysis of high-throughput sequencing data, such as ChIP-seq, RNA-seq or MNase-seq. |
| Insertion-Deletion Calling Workflow for Roddy | Pipeline for detection of high confidence indels (1-20 bp). |
| Roddy | A workflow management system for large scale NGS processing pipelines on Petabyte scale. |
| Transcriptome data analysis | |
| PiGx | Pipeline for the analysis of single-cell RNA-seq data. |
| RNA-Seq End-To-End workflow | Workflow for the gene-level exploratory analysis and differential expression. |
| RNA-Seq pipeline | Pipeline for the analysis of host transcriptome data. |
| ReadXplorer | A software offering straightforward visualization and extensive analysis functions for genomic and transcriptomic DNA sequences mapped on a reference. |
| WASP platform | Platform for the analysis of the scRNA-Seq data. |
| Protein structure analysis |
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| EDIA | Calculates the electron density support for one atom in the model. |
| GeoMine | The first geometric search engine on the entire set of protein-ligand interfaces from the protein database. |
| JAMDA | Molecular docking algorithm. |
| PoseView | Generates high-quality 2D structure-diagrams of protein-ligand complexes provided as 3D-input. |
| Protoss | A fully automated hydrogen prediction tool for protein-ligand complexes. |
| SIENA | A software pipeline enabling the fully automated construction of protein structure ensembles from the protein database. |
| Metabolome data analysis | |
| CellNetAnalyzer | A toolbox for analyzing structure and function of metabolic, signaling, and regulatory networks. |
| Lipidomics | |
| LipidCreator | A lipid building block-based workbench and knowledge base for the semi-automatic generation of targeted lipidomics mass spectrometry assays and in silico spectral libraries. |
| LipidXplorer | Supports bottom-up and top-down shotgun lipidomics experiments performed on all types of tandem mass spectrometers. |
| Modelling of cell biological processes | |
| COPASI | An open-source software application for creating and solving mathematical models of biological processes such as metabolic networks, cell-signaling pathways, regulatory networks or infectious diseases. |
| Data resources | |
| BIONDA | Contains proteins, gene and miRNA marker for human diseases, which are listed in the Uniprot Disease Database. |
| COVID-19 disease map | COVID-19 disease map construction and text mining for drug prediction. |
| FAIRDOMHub | Repository for managing and sharing systems biology research. |
| Galaxy Europe server | Mirrors locally many COVID-19 datasets, allowing for faster analysis. |
| PRIDE | Archive for mass spectrometry-based proteomics data. |
| SABIO-RK | A manually curated database for biochemical reactions and their kinetic properties that is built for the needs of modellers. |
| SEEK | A software platform for collaborative projects to support the data storage and data exchange between project partners. |
