viral-ngs: genomic analysis pipelines for viral sequencing

Contents

• 1. Description of the methods
  • 1.1. Taxonomic read filtration
  • 1.2. Viral genome analysis
  • 1.3. Taxonomic read identification
  • 1.4. Cloud compute implementation
• 2. Installation
  • 2.1. Manual Installation
  • 2.2. Virtualized Installation (Easy Deploy)
• 3. Command line tools
  • 3.1. taxon_filter.py - tools for taxonomic removal or filtration of reads
  • 3.2. assembly.py - de novo assembly
  • 3.3. interhost.py - species and population-level genetic variation
  • 3.4. intrahost.py - within-host genetic variation (iSNVs)
  • 3.5. read_utils.py - utilities that manipulate bam and fastq files
  • 3.6. reports.py - produce various metrics and reports
  • 3.7. illumina.py - for raw Illumina outputs
  • 3.8. broad_utils.py - for data generated at the Broad Institute
• 4. Using the Snakemake pipelines
  • 4.1. Setting up the Python 3 virtual environment
  • 4.2. Setting up an analysis directory
  • 4.3. Running the pipeline
  • 4.4. Assembly of pre-filtered reads
  • 4.5. Taxonomic filtration of raw reads
  • 4.6. Starting from Illumina BCL directories