Ever wondered what M184V, K65R actually mean? I learnt it from rebuilding Stanford’s HIV resistance algorithm from scratch to find out. Spoiler: it took tons of code to match their 3-line tool. But the lesson was worth it. We went from agreement of 89% to 99.8% after different methods of alignment
Learned RNA-seq workflow using C. difficile data from a published study 🧬. Processed raw reads through fastp → kallisto → DESeq2 -> GSEA pipeline. Results matched the original paper’s findings, with clear differential expression between mucus and control conditions 📊.
Hands-on with Oxford Nanopore workflow: pod5 → BAM → assembly! Processed M. tuberculosis from raw signals to complete genome using dorado + flye. Fascinating how thousands of contigs became one 4M+ bp sequence. Polishing question: when is it worth the compute time?
We learnt how to assemble DNA fragments from a recently published N. meningitidis outbreak study using SKESA 🧬, practiced using BLAST for species identification and MLST for strain typing, and explored how serogroups are determined using specialized Python tools for capsule characterization 🔬 - such a fun and exciting hands-on introduction to genomic analysis!
Ever wondered how DNA alignment actually works under the hood? 🧬 We coded the Needleman-Wunsch algorithm from scratch, working through scoring matrices by hand with simple examples like “CAT” vs “CT” before testing on real E. coli sequences. Pretty neat to see the magic happen! ✨