Stenglein Lab Standard Taxonomic Assessment Pipeline Documentation

The Stenglein Lab Standard Taxonomic Assessment Pipeline taxonomically assigns reads in a NGS dataset that remain after filtering host sequences.

This pipeline uses Nextflow, a bioinformatics domain specific language for workflow building. Software dependencies are handled using Docker – a container technology which offers excellent accessibility and reproducibility.

Contents:

• Pipeline Summary
  • Input
  • Quality Assessment and Pre-Processing
  • Host Filtering
  • De novo Assembly of Reads
  • Taxonomic Assessment of Contigs
  • Output
• Software Requirements
• Installation Tutorial
• Running the Pipeline
  • Configuration
  • Docker Profile
  • Usage
• Example Analysis and Output
• References

The Stenglein Lab