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Bioinformatics

Report on prokaryotic genome assembly, Functional Genomics

~6.9k tokens

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.

Comparison of methods in a proteomics benchmark: method comparison, pipeline behavior, and noise analysis using ESM-2

~4.1k tokens

I wanted to test whether my proteomics pipeline can do two things at the same time: - not invent differences where none exist - detect differences where they were deliberately introduced

This dataset is ideal for that purpose, because it is a benchmark with designed true positives (spike-ins) defined by the experiment creators. Below, I show step by step how I verified that the results are trustworthy, and where the pipeline has natural limitations.