pbv

PacBio Validator

Needs assembly sequence and reference sequence to run.

Produces VCF output of duplications in reference genome from insertions found in assembly of genome.

Programs needed (recommended to use conda package manager)

• bedtools
• samtools
• snakemake
• htsbox/dipcall
• lra
• minimap2

programs for hmm caller

• boost
• gcc
• tabix