Content (Syllabus outline)
NGS sequencing platforms: types of technologies and devices, types of NGS libraries, mode of data acquisition and errors.
NGS sequence file formats: SFF, FASTQ, FAST5, UBAM, BAM, SAM. SRA database.
NGS sequence assembly: classical, hybrid methods.
General characteristics of prokaryotic and eukaryotic genomes: size, %GC, GC skew, mutation rate, applicability of oligonucleotide statistics (initiation of chromosome replication, determining the affiliation of species-tetra and laterally transferred chromosome parts, the use in metagenomes -minhash) ...
Sequencing of prokaryotic and eukaryotic genomes: approaches.
Determination of variability between genomes and use of the variability data: determining different alleles, heterozygosity, use in identifying mutations, population analyses.
Single-cell sequencing: single-cell genomics and transcriptomics, methodology, advantages and limitations.
Amplicon sequencing and its use in medicine and biodiversity studies: QIIME2, RAST, OTU and ASV, connections with variability analyses.
Structural and functional annotation of prokaryotic and eukaryotic genomes: structural annotation with and without evidence, approaches to functional annotation (e.g. BLAST, GO, Pfam, KEGG).
Gene prediction without the use of homologies: Genemark (tri-periodic - fifth-order Markov models), Glimmer (interpolated Markov models and context models), GenemarkS (the use of hidden Markov models), Prodigal.
Content and dynamics of prokaryotic genomes:
core in pan-genome; bacterial species delineation; genomic islands and their importance in bacterial evolution; assessment of the frequency of a lateral gene transfer; a tree or a net of life; the link between lifestyle and genomes.
Comparative genomics: what can be compared and how.
Prerequisites
Prerequisites for admittance to final exam:
Practical examination (colloquium)
- presence at at least 80% of practicals.
Exam:
- positive practical examination (colloquium),
- seminar presentation.