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
• 2. Installation
  • 2.1. Cloud compute implementations
  • 2.2. Manual Installation
  • 2.3. Easy deployment script for viral-ngs
• 3. Command line tools
  • 3.1. metagenomics.py - metagenomic analyses
  • 3.2. taxon_filter.py - tools for taxonomic removal or filtration of reads
  • 3.3. assembly.py - de novo assembly
  • 3.4. interhost.py - species and population-level genetic variation
  • 3.5. intrahost.py - within-host genetic variation (iSNVs)
  • 3.6. read_utils.py - utilities that manipulate bam and fastq files
  • 3.7. reports.py - produce various metrics and reports
  • 3.8. illumina.py - for raw Illumina outputs
  • 3.9. broad_utils.py - for data generated at the Broad Institute
  • 3.10. ncbi.py - utilities to interact with NCBI
• 4. Using the WDL pipelines
  • 4.1. Executing WDL workflows locally with Cromwell
  • 4.2. Executing WDL workflows on Google Cloud Platform with Cromwell
  • 4.3. Executing WDL workflows on FireCloud
  • 4.4. Executing WDL workflows on DNAnexus
• 5. Using the Snakemake pipelines
  • 5.1. Installation instructions
  • 5.2. Setting up an analysis directory
  • 5.3. Running the pipeline
  • 5.4. Assembly of pre-filtered reads
  • 5.5. Taxonomic filtration of raw reads
  • 5.6. Starting from Illumina BCL directories
• 6. Developing viral-ngs
  • 6.1. Testing easy_deploy with Vagrant and Ansible