Workshop: Genome assembly with long reads

Day 1

  • - Introduction to NGS (short and long reads)
  • - QC and cleaning  (FastQC, fastplong, MultiQC)
  • - Denovo assembly of prokaryotes with long reads (Hifiasm, Flye, SMRTlink) 
  • we will perform some assembly validation with BUSCO, Bandage, SeqKit, Kraken/Bracken

Day 2

  • - Denovo assembly of eucaryotes with long reads  (Hifiasm)
  • - (optional because difficult: HiC scaffolding with Hifiasm or YAHS)
  • - QC and validation of genome assemblies (completeness, contamination, chromosomes, telomers) (BUSCO, Kraken/Bracken, Merqury, DOT, Tidk, Chromsym, Blobtools).

Day 3 

  • - Genome annotation (repeats, gene prediction, functional prediction) (Prokka, AntiSmash, EDTA, EGAPx, InterProScan)  
  • - Genome browser (IGV)
  • - Conclusion and discussion