Registry Catalogue

Tracy is a command-line tool for the analysis of Sanger chromatogram trace files. It supports basecalling, alignment, assembly, and deconvolution of Sanger sequencing data, enabling robust processing of common capillary sequencing outputs. As part of the GEAR toolbox, Tracy can be used through genome analysis workflows and integrated into automated or reproducible pipelines. Key benefits Processes Sanger chromatogram trace files Supports basecalling and sequence alignment Enables assembly of Sanger sequencing reads Provides deconvolution functionality for mixed trace signals Suitable for integration into command-line and pipeline-based workflows Applications Analysis of Sanger sequencing traces Basecalling from chromatogram files Alignment of Sanger reads to reference sequences Assembly of sequencing reads from capillary sequencing experiments Deconvolution of mixed or overlapping chromatogram signals Intended use Tracy is intended for molecular biologists, geneticists, sequencing facilities, and bioinformaticians working with Sanger sequencing data. It is particularly suited for users who need reproducible command-line processing of chromatogram trace files, either as a standalone tool or as part of broader genome analysis workflows.

Trimmomatic is a flexible and efficient tool for quality trimming and preprocessing of sequencing reads. It removes adapters, trims low-quality bases, and filters reads before downstream analysis. Supporting both single-end and paired-end data, Trimmomatic is widely used as an early quality-control step in reproducible sequencing workflows. Key benefits Fast and configurable preprocessing of sequencing reads Adapter clipping using built-in or user-provided adapter files Quality-based trimming to improve downstream analyses Paired-end aware processing that preserves read pairing Easy integration into automated workflows and HPC environments Applications Preprocessing of reads for genomics, metagenomics, RNA-seq, and amplicon studies Removal of adapters, low-quality bases, and short reads Improving mapping, assembly, and downstream analysis performance Standardized read cleaning in large-scale sequencing workflows Integration into reproducible bioinformatics pipelines Intended use Trimmomatic is intended for bioinformaticians, genomics researchers, sequencing facilities, and life science researchers who need a robust and configurable tool for sequencing read preprocessing. It is particularly suited for users building reproducible sequencing workflows that require reliable adapter removal and quality trimming.

tRNA Database – Collection of Genomic and Mitochondrial tRNAs The tRNA Database provides a comprehensive collection of genomic and mitochondrial transfer RNAs (tRNAs), including their sequences, secondary structures, and genomic locations. It enables researchers to explore and compare tRNA genes across a wide range of organisms, supporting studies in molecular biology, evolution, and functional genomics. Key benefits Centralized repository of genomic and mitochondrial tRNA data Includes sequences, structural information, and genomic coordinates Supports comparative and evolutionary analyses across species Web-accessible resource for quick data retrieval Facilitates research in translation and RNA biology Applications Comparative analysis of tRNA genes across organisms Investigation of tRNA structure and function Studies on mitochondrial and nuclear-encoded tRNAs Annotation and validation of tRNA genes in genomic data Evolutionary analysis of RNA sequences and structures Intended use The tRNA Database is intended for molecular biologists, bioinformaticians, and evolutionary researchers working with RNA sequences and genome annotations. It is particularly suited for users who require structured access to curated tRNA data for analysis and comparison.

TYGS – Type (Strain) Genome Server for Genome-Based Prokaryote Taxonomy TYGS (Type Strain Genome Server) is a web-based platform for genome-based taxonomy of Bacteria and Archaea. Building on the Genome-to-Genome Distance Calculator (GGDC), TYGS provides automated, high-throughput taxonomic analyses using whole-genome comparisons to identify and classify prokaryotic organisms. The platform integrates genome distance calculations, phylogenetic analyses, and comparisons against type strain genomes to support reliable species identification and taxonomic placement. TYGS is complemented by VICTOR for virus phylogeny and classification and is closely linked to the LPSN nomenclature resource. Key benefits Automated genome-based taxonomy for bacteria and archaea High-throughput comparison against type strain genomes Accurate species identification using genome-to-genome distance calculations Phylogenomic tree reconstruction and taxonomic placement User-friendly web interface requiring no local software installation Integration with established resources including GGDC, VICTOR, and LPSN Based on state-of-the-art genome comparison methods replacing conventional DNA–DNA hybridization Applications Identification and classification of bacterial and archaeal isolates Genome-based species delineation Phylogenomic analysis of prokaryotic genomes Taxonomic characterization of newly sequenced isolates Comparative microbial genomics Support for microbial systematics and taxonomy Intended use TYGS is intended for microbiologists, microbial taxonomists, bioinformaticians, and life science researchers working with bacterial and archaeal genome sequences. It is particularly suited for users seeking reliable genome-based species identification, phylogenetic analysis, and taxonomic classification using reference type strain genomes.

Wally is a tool for visualizing aligned sequencing reads and contigs. It supports the inspection of sequence alignments and assembly results, helping users assess read placement, contig structure, and alignment patterns. As part of the GEAR toolbox, Wally complements sequence analysis workflows by providing visual access to aligned genomic data. Key benefits Visualizes aligned sequencing reads and contigs Supports inspection of sequence alignment results Helps assess contig structure and read placement Useful for quality control and interpretation of genome analysis outputs Complements command-line and web-based GEAR workflows Applications Visualization of read alignments Inspection of assembled contigs Quality assessment of sequencing and assembly results Exploration of local alignment patterns Review of genome analysis outputs in research or teaching workflows Intended use Wally is intended for molecular biologists, genomics researchers, sequencing facilities, and bioinformaticians who need to inspect aligned reads or contigs. It is particularly suited for users who want a visual overview of sequencing results to support quality control, troubleshooting, and interpretation.

WebApps provide user-friendly, web-based access to mass spectrometry data analysis and visualization workflows built using the OpenMS ecosystem. The service enables researchers to process, inspect, and interpret MS-based proteomics, metabolomics, and related omics data directly through interactive browser interfaces, without requiring local software installation or command-line expertise. The platform is designed to make advanced OpenMS functionality more accessible to life scientists, bioinformaticians, and method developers. It supports interactive data exploration, visual quality control, workflow execution, and result inspection in a reproducible and shareable environment. By combining established OpenMS algorithms with modern web technologies, the WebApps lowers the barrier for applying computational mass spectrometry methods in research, teaching, and collaborative projects. Typical use cases include interactive visualization of spectra and identifications, exploration of search results, quality control reporting, targeted workflow interfaces, and educational demonstrations. The service can also serve as a template for developing specialized web applications around OpenMS tools and workflows. Key features: - Web-based access to OpenMS-powered MS analysis tools - Interactive visualization and inspection of mass spectrometry data - No local installation required for end users - Support for reproducible and shareable analysis sessions - Extensible framework for building domain-specific MS web applications - Suitable for research, teaching, and training Target users: OpenMS WebApps is intended for experimental scientists, bioinformaticians, software developers, and educators who want accessible, interactive, and reproducible tools for computational mass spectrometry. For a full list of provided WebApps visit: https://openms.de/

WESkit is an implementation of the Workflow Execution Service (WES) API defined by the Global Alliance for Genomics and Health (GA4GH). It provides a standardized, programmatic interface to submit, monitor, and manage computational workflows across different execution environments. By exposing workflow execution through a common API, WESkit supports interoperable workflow services for bioinformatics, genomics, and federated research infrastructures. Key benefits Standards-based implementation of the GA4GH WES specification Unified API for workflow submission, monitoring, and management Backend-agnostic design for different workflow engines and compute infrastructures Suitable for local systems, HPC clusters, and cloud environments Supports automation and integration into larger research platforms Applications Deployment of interoperable workflow execution services Standardized execution of genomics and bioinformatics pipelines Integration of workflow engines with institutional or federated infrastructures Automated submission and monitoring of computational analyses Platform development for cloud, HPC, or hybrid research environments Intended use WESkit is intended for infrastructure developers, platform engineers, bioinformatics service providers, and workflow system developers who want to expose workflow execution capabilities through a GA4GH-compliant interface. It is particularly suited for projects that require standardized, programmatic workflow control across heterogeneous compute backends.