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