~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.
~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.
~2.1k tokens
I have been working on several interesting projects, and some of them may come to fruition this year. Unfortunately, because the groups in our environment are relatively small, progress has been slower than expected. The tasks have also become harder, with fewer options to expand the work or speed things up. Instead of having six or seven people working in parallel, most efforts have been carried by much smaller teams.