Report on prokaryotic genome assembly, Functional Genomics
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This post walks through an end to end Nanopore assembly of a Bacillus subtilis sized bacterial genome: read QC, reference mapping sanity checks, de novo assembly with Flye, assembly graph inspection in Bandage, quality assessment with QUAST and CheckM, and final annotation with Prokka. The emphasis is on showing why each step exists and how to interpret the key outputs, not on chasing maximum performance.