Sep 23, 2021 · In this Perspective, we highlight key features of workflow managers, compare commonly used approaches for bioinformatics workflows, and provide a guide for computational and noncomputational...

Jan 26, 2025 · Results We present BioMaster, a multi-agent framework designed to automate and streamline complex bioinformatics workflows. BioMaster incorporates specialized agents with role-based responsibilities, enabling precise task decomposition, execution, and validation.

We then highlight the benefits of using scientific workflow systems to get modular, reproducible and reusable bioinformatics data analysis pipelines. We finally discuss current workflow reuse practices based on an empirical study we performed on a large collection of workflows.

In this work, a bioinformatics workflow for (Illumina) WGS data is presented for bacterial characterisation including genome annotation, species identification, serotype prediction, antimicrobial resistance prediction, virulence-related genes and plasmid replicon detection, core-genome-based or single nucleotide polymorphism (SNP)-based phylogen...

Metabolomics is an emerging field that quantifies numerous metabolites systematically. The key purpose of metabolomics is to identify the metabolites corresponding to each biological phenotype, and then provide an analysis of the mechanisms involved.

Apr 3, 2025 · The Playbook Workflow Builder (PWB) is a web-based platform to dynamically construct and execute bioinformatics workflows by utilizing a growing network of input datasets, semantically annotated API endpoints, and data visualization tools contributed by an ecosystem of …

Nov 29, 2018 · H3ABioNet has built four workflows to support (1) the calling of variants from high-throughput sequencing data; (2) the analysis of microbial populations from 16S rDNA sequence data; (3) genotyping and genome-wide association studies; and (4) single nucleotide polymorphism imputation.

We encourage you to discuss the experimental design with the person who will analyse the data (or with NBIS)! Design and Technical aspects Choice of experimental setup Low-input bulk RNA-seq Single cell RNA-seq Formulating the scientific question and means to address it . 1.

Here we provide basic proof-of-concept implementations for selected workflow managers. The analysis workflow is based on a small portion of an RNA-seq pipeline, using fastqc for quality controls and salmon for transcript quantification. These implementations are …

Apr 26, 2025 · IMP provides a workflow that can handle both metagenomic and metatranscriptomic data, supporting reference genome-independent analysis methods, but its analysis speed is relatively slow, especially with complex samples, and it poses a learning curve for users without a bioinformatics background.