Monday. Classes from 2 to 8 pm Berlin time

 

-       Genomes

 

-       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