Project plan

2026-04-12 - 2026-04-15 Genome assembly

• Assemble genome with PacBio reads (Canu)
• Assemble genome with Nanopore + Illumina (Spades, optional)

2026-04-16 - 2026-04-27 Genome evaluation & annotating

• Genome assembly evaluation (QUAST)
• Genome assembly evaluation (BUSCO, optional)
• Genome annotation (Prokka)
• Find related species (BLAST?)
• Synteny comparison (MUMerplot, related species)

2026-05-06 - 2026-05-10 RNA mapping

• RNA QC & trimming (FASTQC -> TRIMMOMATIC -> FASTQC)
• RNA alignment against assembled genome (BWA)

2026-05-12 - 2026-05-20 Interpretation

• Read counting (HTSeq)
• Differential expression of RNA, "human_serum - BHI_medium" (DESeq2)
• GSEA (???, optional)

2026-05-21 - 2026-05-25 Finalize wiki & presentation

• Fix wiki
• Make presentation