viral-ngs: genomic analysis pipelines for viral sequencing

Contents

• 1. Description of the methods
• 2. Command line tools
  • 2.1. illumina.py - for raw Illumina outputs
  • 2.2. read_utils.py - utilities that manipulate bam and fastq files
  • 2.3. assembly.py - viral sequence assembly from NGS reads
  • 2.4. taxon_filter.py - filter reads by taxonomic membership
  • 2.5. metagenomics.py - utilities for metagenomic analyses
  • 2.6. kmer_utils.py - commands for working with sets of kmers
  • 2.7. interhost.py - SNP calling, multi-alignment, and phylogenetics
  • 2.8. intrahost.py - intrahost variant calling and annotation
  • 2.9. ncbi.py - NCBI Genbank and SRA utilities
  • 2.10. reports.py - produce various metrics and reports
  • 2.11. file_utils.py - utilities to perform various file manipulations
  • 2.12. broad_utils.py - for data generated at the Broad Institute