viral-ngs: genomic analysis pipelines for viral sequencing¶
Contents¶
- 1. Description of the methods
- 2. Installation
- 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
- 5. Using the Snakemake pipelines
- 6. Developing viral-ngs