Data analysis

Quality profiles

• De-multiplexing: remove barcode sequences
• Trimming: remove the primer and adaptor sequences from raw reads
• Filtering: filter low-quality sequences of both forward and reverse reads, which are unexpected reads
  

Genome assembly

• Unicycler : an assembly pipeline for bacterial genome
• QUAST : evaluate the quality of assembled genome
  

Genome annotation

• Prokka : rapid prokaryotic genome annotation
  

Species identification and Phylogenetic tree analysis

• Calculate average nucleotide identity (ANI) based on a BLAST algorithm and Tetra Correlation Search (TCS) function
• High-resolution of phylogenetic tree: multi-Locus Sequence Analysis (MLSA) method with automatic selection of reference genomes

Bacterial variant calling

• Identify single-nucleotide polymorphisms (SNPs) from bacterial sequencing data base on reference mapping
   

Functional characterization of genome

• Perform KO (KEGG Orthology) assignments to characterize individual gene functions and reconstruct Kyoto Encyclopedia of Genes and Genomes, KEGG pathways, BRITE hierarchies and KEGG modules to infer high-level functions of the organism
  
  

Specialty genes and antimicrobial resistance gene (AMR) analysis

• Provide in silico antibiograms which assign to each AMR gene functional annotation and specific antibiotic is conferring resistance to
  
  

Secondary metabolite prediction

• Identify and annotate secondary metabolite biosynthesis genome mining in bacterial genome
  
  

Phage sequence identification

• Phage search tool (PHAST): search and identify prophage sequences within bacterial genomes or plasmids
  
  

Phylogeny analysis

• Show a simple branching diagram that represents the evolutionary relationships among species, organisms, or genes from a common ancestor

Bacterial comparative genomics

• Comparison of biological information derived from WGS. Whole gene sets are compared to elucidate the common and different genomic features among two or more target organisms.