Genome Assembly, осень 2014
Курс: Биоинформатика.
Преподаватель: Яна Сафонова.
Ассистенты: Антон Банкевич.
Даты: Sep 2014 — Nov 2014.
Программа курса:
- Genome assembly problem overview. Applications of genome assembly. Characteristics of sequencing technologies. Sequencing materials. Basic approaches: OLC and de Bruijn graphs.
- Read correction tools. Quality assessment of genome assembly.
- Overlap Layout Consensus approach. ARACHE and Celera assemblers. Their application to Sanger and Pacbio reads. Novel approaches based on OLC.
- De Bruijn graph approach. Velvet, SPAdes, ABySS and other de Bruijn graph assemblers. Some theoretical constructions. Effective construction of de Bruijn graph.
- Repeats are bottleneck of de novo genome assembly. Repeat resolution algorithms. exSPAnder. Ray. Telescoper. Some theoretical constructions.
- Reference-assisted assembly.
- How can we deal with mammalian and plant size genomes? Minia, MaSuRCA, JR-Assembler. Some examples.
- Assembly of diploid genome. Inbreeding. Hapsembler, HaploMerger, dipSPAdes.
- Haplotype assembly. HapCUT, HapCompass, extensions for polyploid cases.
- Story of two genomes, Ciona savignyi and Ciona intestinalis: from sequencing to finishing.
- Assembly of metagenomics data.
- Reconstruction of ancestral genome.