SOP of bacteria sequencing analysis

Quality control

• QC tools (FastQC, MultiQC …)

• Is coverage enough ?

• Is length read length enough ?

• Is there contamination ?

Assembly

• Assembler tools (Canu, Unicycler, Flye, Ra …)

• Genome Polishing (Racon, medaka, nanopolish …)

• Plasmid check(BLAST)

Genome annotation

• NCBI annotation

• COG analysis for protein functions

16S rRNA/whole genome phylogenetic trees

Antibiotic-resistant gene prediction

Virulence gene prediction