Whole Genome Sequencing Pipeline Overview
- Handles both Illumina paired-end and Nanopore reads
- Performs initial quality assessment of input reads
- Supports multiple reference genomes including H37Rv, Smeg, Bovis, and others
- Uses BWA-MEM for Illumina reads alignment
- Uses Minimap2 for Nanopore reads alignment
- Generates sorted and indexed BAM files
- Produces alignment statistics and coverage metrics
- Uses BCFtools mpileup for initial variant detection
- Employs Freebayes as secondary variant caller
- Generates detailed VCF files with variant information
- Includes quality scores and read depth information
- Generates coverage plots and statistics
- Creates detailed alignment reports
- Produces MultiQC summary reports
- Results delivered via email upon completion