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   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.


   Download WGS Report


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