Monday. Classes from 2 to 8 pm Berlin time
- Sequencing technologies
- Genome assembly
- Hands on: Introduction to Linux – manipulating reads files
Tuesday. Classes from 2 to 8 pm Berlin time
- What are reads k-mers?
- K-mer analysis: estimating genome size, heterozygosity and repeat content
- Plotting k-mer profiles
- Presentation of different assembly algorithms: Hicanu, wtdbg2, falcon, hifiasm
- Start assembling different small eukaryotic genomes: butterflies, moths and others.
Wednesday. Classes from 2 to 8 pm Berlin time
- Purging haplotigs: what Is that about?
- Purging assemblies
- Evaluation of purged assemblies: contiguity (N50, total length), accuracy (merqury k-mer evaluation) and gene content (BUSCO) analysis
- Start polishing and/or HiC scaffolding
Thursday. Classes from 2 to 8 pm Berlin time
- What is Hi-C sequencing? Theory and practice
- Hands on time to run analysis on Hi-C scaffolded assemblies: evaluate final contiguity, accuracy and gene content
Friday. Classes from 2 to 8 pm Berlin time
- Finishing up analysis. Even though we will be online, different groups of participants will work on the same data, so they will have a few hours to discuss the results and prepare a final presentation.
- General discussion
- Final questions
- Online drink, alcoholic or otherwise