GETTING STARTED
Welcome to Bioxflow
Bioxflow is being developed as a bioinformatics platform for reproducible computational biology and genomic data analysis. Our goal is to make computational workflows easier to understand, execute, reproduce and extend.
This documentation introduces the technologies, methods and workflow concepts behind the platform. It will expand as individual pipelines are developed, tested and released.
A note about workflow availability
Some guides currently describe planned or illustrative workflows. Always check the relevant project repository for implementation status, tested versions and validated instructions before running an analysis.
SETTING UP YOUR ENVIRONMENT
Installation and prerequisites
Bioinformatics workflows often require several software tools and dependencies. Before running a workflow, check its individual requirements and supported operating systems.
Recommended tools
These are general recommendations. Individual workflows may have additional software and hardware requirements.
YOUR FIRST WORKFLOW
Quick start
A typical bioinformatics workflow begins with raw sequencing data, applies quality control and preprocessing, and generates analysis results and reports.
Example project setup
mkdir my-bioinformatics-project
cd my-bioinformatics-project
mkdir data results scripts reports
# Keep your input FASTQ files in data/
# Store analysis outputs in results/
# Store workflow scripts in scripts/Example project structure
my-bioinformatics-project/
├── data/
├── results/
├── scripts/
├── reports/
└── README.mdThis is a generic project structure, not an executable Bioxflow pipeline. Follow the relevant pipeline guide when a workflow becomes available.
WORKFLOW TECHNOLOGIES
Nextflow
Nextflow is a workflow management system used to build scalable and reproducible data analysis pipelines. It supports execution across local computers, HPC systems and cloud environments.
Check your installation
nextflow -versionNextflow requires a compatible Java installation. Consult the official Nextflow documentation for current installation and compatibility instructions.
Official Nextflow documentation →Snakemake
Snakemake is a workflow management system that uses rule-based definitions to connect input files, computational steps and output files. It is particularly useful for creating modular, reproducible research workflows.
Check your installation
snakemake --versionComputational environments
Managing software versions is essential for reproducible bioinformatics. Conda, Mamba and containers can help researchers manage dependencies and reduce conflicts between tools.
Conda / Mamba
Manage software packages and isolated environments.
Docker
Package applications and their dependencies into containers.
PIPELINE GUIDES
Whole-genome sequencing
Whole-genome sequencing analysis investigates the genetic composition of an organism using sequencing data. A typical short-read analysis may include quality control, trimming, alignment, variant calling and annotation.
Typical analysis stages
- 01 — Raw read quality assessment
- 02 — Adapter and quality trimming
- 03 — Reference genome alignment
- 04 — Alignment processing and quality checks
- 05 — Variant calling
- 06 — Variant annotation and reporting
Workflow implementation and supported data types will be documented in the corresponding project repository.
RNA-seq analysis
RNA sequencing enables researchers to investigate gene expression and transcriptional changes across biological conditions.
Typical analysis stages
- 01 — FASTQ quality control
- 02 — Adapter trimming and filtering
- 03 — Read alignment or transcript quantification
- 04 — Gene-level count generation
- 05 — Differential expression analysis
- 06 — Functional enrichment and visualisation
Tools and methods depend on the experimental design, organism and sequencing strategy.
The Bioxflow Bulk RNA-seq pipeline (v1.0.0) is available →Antimicrobial resistance genomics
AMR genomics uses bacterial sequencing data to investigate antimicrobial resistance determinants, virulence factors, plasmids and genetic relationships between isolates.
Potential analysis components
- • Genome assembly and quality assessment
- • Species identification and genome annotation
- • Antimicrobial resistance gene screening
- • Virulence factor identification
- • Plasmid and mobile genetic element analysis
- • Comparative genomics and reporting
HELP & RESOURCES
Troubleshooting
Command not found
Check whether the software is installed and whether its executable is available in your system PATH.
Dependency conflicts
Check the workflow environment configuration and software version requirements. Use an isolated environment where appropriate.
Workflow execution fails
Review the execution log, input file paths, resource requirements and configuration parameters.
Contributing to Bioxflow
Bioxflow aims to encourage collaboration in computational biology. Contributions may include workflow development, documentation, testing, bug reports and scientific feedback.
Learn how to contribute →CONTINUE EXPLORING
Ready to explore our workflows?
Visit the Pipelines section to explore Bioxflow's workflow categories and development roadmap.
Explore pipelines →