sbx_induceome is a sunbeam extension for identifying induced, (previously) integrated phages. This pipeline uses bwa for alignment to the host and samtools to find the induced sites.
NOTE: sbx_induceome makes a couple assumptions about your reference genomes and reads. It assumes that 1) the reference files are named cd{number}.fas (under the directory you specify in the config) and 2) the read files are formatted like ...T{number}_....fastq.gz (the ... here can be whatever other characters you have in your sample name, although be careful not to include other instances of T{number}_).
- threads: Number of cores to use when running bwa
- reference_fp: Directory with reference genomes
- mapping_fp: Path to the file mapping samples to strains (.csv)
- blast_db: Path to the viral blast db (full path including .faa file name)
- pharokka_db: Path to the pharokka db (full path to the directory that will hold db files)
- phold_db: Path to the phold db (full path to the directory that will hold the tsv and other db files)
- min_width: The sliding window size for peak finding
- smoothing_factor: The number of below-threshold sliding windows to tolerate as being part of one peak
More docs.