PGCGAP is a pipeline for prokaryotic comparative genomics analysis. It can take the pair-end reads, Oxford reads or PacBio reads as input. In addition to genome assembly, gene prediction and annotation, it can also get common comparative genomics analysis results such as phylogenetic trees of single-core proteins and core SNPs, pan-genome, whole-genome Average Nucleotide Identity (ANI), orthogroups and orthologs, COG annotations, substitutions (SNPs) and insertions/deletions (indels) with only one line of commands.

We have written an article introducing the basics of Linux, usage of common commands, software installation, and the whole-genome sequencing technology was written to help users get started with bioinformatics.