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