HybSeq course 2020
20.01.2020 09:00 až
|Místo||Seminárium, Benátská 2, Praha 2|
|Přidat událost do kalendáře||
vKalendář (Windows, Linux)
iCal (Mac OS X)
Participants will become familiar with all theory about HybSeq: Participants will get an introduction to HybSeq and learn about the advantages and disadvantages of target enrichment vs. other genome sub-selection methods such as RADseq. We will discuss about the proper selection of genomic targets (the so-called probe design) and the pros and cons of group-specific vs. universal probes. Additional datasets that can be obtained with HybSeq will be highlighted and, finally, a summary of the wet lab workflow of target enrichment will be given.
Participants will understand principles of computational data analysis, i.e. how and why are the raw FASTQ files prepared (trimming, deduplication, quality checking) and processed by HybPiper, aligned and how gene and species trees are constructed.
Participants will have sufficient knowledge to be able to run all steps on a cluster using Linux command line and will be able to deal with all common technical issues.
Participants will be able to deal with all major problems of species tree construction, i.e. main source of gene trees incongruences and how do deal with them, how to evaluate differences among gene trees, etc.
All theory about HybSeq, target enrichment, etc. — introduction to HybSeq, advantages and disadvantages of target enrichment vs. other genome sub-selection methods, selection of genomic targets (probe design), group-specific vs. universal probes, additional datasets that can be obtained with HybSeq, target enrichment wet lab workflow.
All scripting and data processing — trimming, deduplication, running HyPiper, aligning contigs, gene and species trees constructions, etc.
ASTRAL (including multilocus bootstrapping, local posterior probability, hard polytomy testing, hypothesis scoring...), supertree methods (MRL etc.), and more.
All information about the course, including application form etc. can be found at https://trapa.cz/cs/hybseq-course-2020