Registry Catalogue

ACEseq (Allele-specific copy number estimation with whole genome sequencing) is a tool for estimating allele-specific copy numbers from human whole-genome sequencing data. It supports copy number analysis in tumour genomes and includes GC and replication timing bias correction, quality control, structural variant breakpoint integration, and automated estimation of ploidy and tumour cell content. ACEseq can be used with or without matched control samples. Key benefits Estimates allele-specific copy numbers from human WGS data Supports tumour genome analysis with or without matched controls Includes GC and replication timing bias correction Provides quality checks and structural variant breakpoint inclusion Supports automated estimation of ploidy, tumour cell content, and genomic instability scores Applications Allele-specific copy number analysis in cancer genomes Whole-genome sequencing analysis of tumour samples Estimation of ploidy and tumour cell content Integration of structural variant breakpoints into copy number analysis Calculation of HRD, TAI, and LST scores for genomic instability assessment Intended use ACEseq is intended for cancer genomics researchers, bioinformaticians, sequencing facilities, and clinical research groups working with human whole-genome sequencing data. It is particularly suited for projects that require allele-specific copy number estimation, tumour purity and ploidy assessment, or integration of copy number and structural variant information in WGS-based cancer genome analysis.

Alfred is a comprehensive tool for quality control of next-generation sequencing alignments. It supports commonly used alignment QC metrics, RNA and DNA feature counting, and flexible feature annotation. As part of the GEAR toolbox, Alfred helps users evaluate sequencing data quality and generate quantitative summaries from aligned NGS datasets. Key benefits Provides comprehensive quality control for NGS alignments Supports commonly used alignment QC metrics Enables RNA and DNA feature counting Offers flexible feature annotation options Suitable for reproducible command-line and pipeline-based analyses Applications Quality control of NGS alignment files Assessment of sequencing and mapping performance RNA and DNA feature counting Generation of summary metrics for sequencing datasets Integration into automated NGS analysis workflows Intended use Alfred is intended for bioinformaticians, genomics researchers, sequencing facilities, and life science researchers working with aligned NGS data. It is particularly suited for users who need reproducible alignment quality control, feature counting, and reporting within genome, transcriptome, or other sequencing analysis pipelines.

AlignmentAndQCWorkflows provides Roddy-based workflows for alignment and quality control of next-generation sequencing data. The plug-in includes workflows for whole-genome sequencing, whole-exome sequencing, and whole-genome bisulfite sequencing that are based on BWA MEM alignments. The workflows include extensive quality control steps for BAM files, using parallelized piping into multiple QC tools to improve performance. Key benefits Provides Roddy-compatible workflows for NGS alignment and quality control Supports WGS, WES, and WGBS data processing Includes PanCancer alignment workflows for genome and exome data Provides a bisulfite core workflow using methylCtools Optimized BAM-level quality control through high-performance I/O minimizing processing Applications Alignment of whole-genome and targeted sequencing data, such as whole-exome sequencing Processing of whole-genome bisulfite sequencing datasets Quality control of aligned BAM files Analysis of individual samples or tumor–control sample combinations Integration into Roddy-based standardized NGS processing pipelines Stand-alone and or as alignment workflow for the One-Touch-Pipeline (OTP) workflow automation management platform Intended use AlignmentAndQCWorkflows is intended for bioinformaticians, genomics researchers, sequencing facilities, and infrastructure teams working with human NGS datasets. It is particularly suited for users who need performant, standardized, and BWA-based alignments, BAM-level quality control, and processing of WGS, WES, or WGBS data in reproducible analysis environments.

BacDive (The Bacterial Diversity Database) is the world’s largest knowledge base of standardized, strain-level bacterial and archaeal information. Recognized as both an ELIXIR Core Data Resource and a Global Core Biodata Resource, BacDive mobilizes and makes freely available research data from culture collections, species descriptions, and other curated sources. The database currently contains more than three million data points on over 100,000 strains, covering taxonomy, morphology, physiology, metabolism, origin, biosafety, sequence data, and cultivation. Key benefits Comprehensive strain-level information for more than 100,000 bacterial and archaeal strains More than 1,000 standardized data fields across a broad range of biological and experimental topics Manually curated data from species descriptions and international culture collections Powerful search tools for identifying strains by phenotype, growth conditions, habitat, or isolation source Programmatic access through a RESTful API and SPARQL endpoint Recognized as an ELIXIR Core Data Resource and a Global Core Biodata Resource Applications Identification of strains with specific physiological or metabolic characteristics Search for organisms isolated from particular environments or host-associated habitats Selection of strains for cultivation and experimental studies Comparative analysis of microbial traits and phenotypes Linking strain-level information with sequence and biosafety data Large-scale data retrieval and knowledge-graph-based analyses via API or SPARQL Intended use BacDive is intended for microbiologists, microbial ecologists, taxonomists, bioinformaticians, data scientists, and biotechnology researchers who require comprehensive and standardized information on bacterial and archaeal strains. It is particularly suited for users searching for strains with defined biological characteristics or integrating curated strain-level data into large-scale computational analyses.

BakRep is a comprehensive, scalable web repository that aggregates and standardizes millions of publicly available bacterial genomes from e.g. AllTheBacteria. Each genome is enriched with uniform quality metrics, taxonomic classification, sequence typing, and annotation, enabling rapid and reproducible comparative analyses across large datasets, and integrated with accompanying submission metadata. Key Benefits Extensive data coverage with consistently processed bacterial genomes. Integrated Metadata: original submission metadata comprising e.g. sampling location, data, source. Standardized genome characterizations, including QC, taxonomy, MLST, and annotation. Powerful search and filtering to compile custom genome sets based on genomic or metadata attributes. Web interface and command-line access for both exploratory and automated high-throughput workflows. Features Unified pipeline for QC, taxonomic assignment, sequence typing, and annotation. Advanced search by species, genome size, GC content, contig count, sequence type, and more. Downloadable genome subsets for downstream computational analyses. CLI integration for large-scale or reproducible workflows. Applications Comparative genomics, phylogenetics, and population genomics. Large-scale surveys of resistance genes, virulence factors, or metabolic traits. Building curated genome datasets for benchmarking or tool development. Supporting epidemiological investigations and outbreak analyses. Intended Use BakRep is ideal for microbial genomics researchers, bioinformaticians, and epidemiologists who need reliable, standardized access to large bacterial genome collections.

Bakta is a tool for rapid and standardized annotation of bacterial genomes and plasmids from isolates and metagenome-assembled genomes (MAGs). It provides taxon-independent annotations enriched with database cross-references, including small open reading frames (sORFs), and outputs results in machine-readable JSON as well as common bioinformatics file formats for automated downstream analysis. Bakta is available both as a scalable web application and as a local command-line tool via Docker and Conda. Key benefits Rapid and standardized annotation of bacterial genomes, plasmids, and MAGs Taxon-independent workflow suitable for diverse bacterial datasets DBXref-rich annotations supporting downstream interpretation Includes small open reading frames (sORFs) in the annotation process Available as web application and local command-line tool Applications Annotation of bacterial isolate genomes Annotation of plasmids and metagenome-assembled genomes Preparation of standardized genome annotation files for downstream workflows Comparative bacterial genomics and genome characterization Integration into automated bioinformatics pipelines Intended use Bakta is intended for microbiologists, microbial genomicists, bioinformaticians, and researchers working with bacterial genome data. It is particularly suited for users who need fast, reproducible, and standardized genome annotations for isolates, plasmids, or MAGs, either through an accessible web interface or local command-line workflows.

BAND (Bioimage Analysis Desktop) and BARD (Bioimage Analysis Research Desktop) provide cloud-based desktop environments for bioimage analysis, accessible directly through a web browser. Applications run in fully containerized environments orchestrated by OpenStack or Kubernetes clusters, enabling users to work with GUI-based imaging tools without local installation or complex infrastructure setup. BAND/BARD are designed for both individual image analysts and course organizers who require scalable computational resources for hands-on training. The de.NBI BAND instance is hosted at the de.NBI Tübingen node and offers configurable desktops with CPU, RAM, and GPU resources. Key benefits Browser-based access to desktop environments with containerized bioimage analysis software No local installation of complex imaging software required Configurable compute resources including CPU, RAM, and GPU options Suitable for scalable training courses and workshops Persistent user storage with options to access external data sources Applications Running GUI-based bioimage analysis applications in the cloud Providing standardized desktop environments for training events Interactive image analysis without maintaining local workstations GPU-supported analysis workflows where available Accessing remote datasets through integrated tools such as Rclone Intended use BAND/BARD are intended for image analysts, bioimage researchers, trainers, course organizers, and life science researchers who need browser-accessible computing environments for image analysis. They are particularly suited for users who rely on graphical software tools, require scalable compute resources for training, or want to provide standardized analysis environments to multiple participants.

The Berlin RNA Toolbox is a comprehensive collection of bioinformatics tools and databases. The toolbox offers a wide range of resources for researchers to analyze, predict, and understand various aspects of RNA biology. Key Benefits Comprehensive analysis of RNA interactions : Identify potential binding sites of microRNAs on messenger RNAs (mRNAs) and explore the complex relationships between RNAs. In-depth analysis of circular RNAs : Discover circRNAs in RNA-seq data and explore their potential functions. Accurate prediction of protein-RNA interactions : Identify specific binding regions between proteins and RNAs. Tools PicTar : A microRNA target predictor that identifies potential binding sites of microRNAs on messenger RNAs (mRNAs). miRDeep : A probabilistic model that detects the presence of expressed animal microRNAs in deep sequencing data. PIPmiR : A tool to identify novel plant miRNA genes from a combination of deep sequencing and genomic features. NASTIseq : Expression analysis for the identification of cis-Natural Antisense Transcripts (cis-NAT) from strand-specific RNA-seq data. PARalyzer : A peak finder for protein-RNA interaction sites in PAR-CLIP data, helping to identify specific binding regions between proteins and RNAs. microMUMMIE : MicroRNA target-site prediction in PAR-CLIP data, allowing researchers to predict potential microRNA binding sites within PAR-CLIP peaks. cERMIT : A motif finder for large sequence sets e.g. from chromatin or RNA immunoprecipitation experiments, enabling users to identify conserved motifs across different sequences. Databases doRiNA : A database of RNA interactions in post-transcriptional regulation, providing insights into the complex relationships between RNAs. circBase : A database for public circular RNA datasets, allowing users to discover circRNAs in RNA-seq data and explore their potential functions. Target Audience The Berlin RNA Toolbox is designed for researchers in the fields of molecular biology, bioinformatics, and computational biology. The tools and databases provided are particularly useful for scientists interested in understanding various aspects of RNA biology, including microRNA regulation, circular RNAs, and protein-RNA interactions.

bHLH Annotator is a web-based tool for the automated identification and functional annotation of the basic Helix–Loop–Helix (bHLH) transcription factor family in plants. The tool analyzes coding or protein sequences derived from genome or transcriptome assemblies and combines homology searches, phylogenetic analysis, orthology inference, and motif detection to provide reliable functional annotations. By automating the annotation workflow, bHLH Annotator enables rapid and reproducible characterization of bHLH gene families in newly sequenced plant species. Key benefits Automated identification of plant bHLH transcription factors Functional annotation based on orthology to experimentally characterized bHLHs Combines BLAST or HMMER searches with phylogenetic classification Detects conserved bHLH domains, DNA-binding properties, and subfamily-specific motifs Supports genome and transcriptome assemblies Web-based service with reproducible analysis workflow Applications Annotation of bHLH gene families in newly sequenced plant genomes Functional characterization of transcription factors Comparative genomics of plant transcription factor families Evolutionary and phylogenetic analyses of bHLH proteins Candidate gene identification for plant functional genomics Analysis of de novo genome and transcriptome assemblies Intended use The bHLH Annotator is intended for plant biologists, genome annotation specialists, bioinformaticians, and evolutionary researchers working with plant genome or transcriptome data. It is particularly suited for researchers who require accurate and automated annotation of bHLH transcription factors for comparative genomics, gene family evolution, and functional genomics studies.

BiBiServ Tools is the bioinformatics web service platform of the Bielefeld Institute for Bioinformatics Infrastructure at CeBiTec, Bielefeld University. It provides long-term online access to research software as software as a service and makes more than 50 bioinformatics tools available for academic use. The platform covers a broad range of life science applications, including sequence analysis, multiple sequence alignment, RNA structure prediction, comparative genomics, genome evolution, motif analysis, primer design, phylogenetics, metatranscriptomics, single-cell genomics, and gene cluster detection. Key benefits Provides web-based access to a broad portfolio of bioinformatics tools Supports long-term availability of research software as online services Covers sequence, genome, transcriptome, RNA, and omics-related analyses Includes tools developed at Bielefeld University and by partner groups Enables academic users to run analyses without local installation Applications Sequence analysis, multiple sequence alignment, and motif search Comparative genomics, genome rearrangement, and genome evolution analysis RNA structure prediction and RNA interaction analysis Primer design, phylogenetics, and gene cluster detection Metatranscriptomics, single-cell genomics, and immune repertoire analysis Included tool areas Sequence alignment and comparison – tools such as ClustalW, DIALIGN, DCA, AltAVist, JAli, OMA, MGA, SWIFT, and mmfind Comparative genomics and genome rearrangement – tools such as E2G, AGenDA, CG-CAT, UniMoG, CEGeD, Roci, ROCOCO, FFGC, Gecko2, GEvolutionS, newdist, and REPuter Motif and protein family analysis – tools such as PoSSuMsearch, PoSSuMsearch2, jPREdictor, PREdictor, MoRAine, and ConCysFind RNA bioinformatics – tools such as RNAshapes, RNAalishapes, pKiss, pAliKiss, pknotsRG, RNAforester, RNAhybrid, Locomotif, paRNAss, RapidShapes, GUUGle, InSilicoDicer, and aCMs Specialized analysis tools – including genefisher2, Acdc, SciBrow, Metrans, TCRProfiler, Intronserter, AIM, and AGT-SDP Intended use BiBiServ Tools is intended for bioinformaticians, molecular biologists, genomics researchers, RNA researchers, computational biologists, and academic life science users who need accessible online tools for biological sequence, genome, transcriptome, RNA structure, or related omics analyses. It is particularly suited for users who want to access established research software through a web interface without installing and maintaining the tools locally.

BIIGLE is a web-based software for image and video annotation that enables collaborative research on large datasets. It offers tools for manual and computer-assisted annotation, quality control and the collaboration on custom taxonomies to describe objects. BIIGLE is freely available and can be installed in cloud environments, a local network or on mobile platforms during research expeditions. The public instance on biigle.de is free for non-commercial use.

Bioconda is a community-driven software distribution for bioinformatics and life-science tools based on the Conda package manager. It provides easy access to thousands of curated software packages and supports reproducible installation and management of complex bioinformatics workflows. Bioconda packages are tightly integrated with BioContainers, enabling container-based execution of the same software. Key Benefits: Simple installation with automatic dependency resolution. Reproducible environments through versioned packages and containers. Broad coverage across genomics, transcriptomics, metagenomics, proteomics, and systems biology. Flexible execution via Conda environments or containers. Suitable for local systems, HPC, and cloud infrastructures. Features: Large, community-maintained repository of bioinformatics software packages. Automated building and testing to improve consistency and reliability. Generation of BioContainers from Bioconda packages for container-based workflows. Support for isolated Conda environments and container runtimes. Compatibility with Linux and macOS systems. Applications: Installation and management of bioinformatics software stacks. Building reproducible analysis environments for research and training. Running workflows in container-based systems and workflow managers. Standard software provisioning in research infrastructures and core facilities. Intended Use: For bioinformaticians, life-science researchers, and infrastructure providers who need reliable, reproducible software installation. Supports both Conda-based environments and containerized execution using BioContainers.