Genome Assembly, осень 2014

Курс: Биоинформатика.

Преподаватель: Яна Сафонова.

Ассистенты: Антон Банкевич.

Даты: Sep 2014 — Nov 2014.

Программа курса:

  1. Genome assembly problem overview. Applications of genome assembly. Characteristics of sequencing technologies. Sequencing materials. Basic approaches: OLC and de Bruijn graphs.
  2. Read correction tools. Quality assessment of genome assembly.  
  3. Overlap Layout Consensus approach. ARACHE and Celera assemblers. Their application to Sanger and Pacbio reads. Novel approaches based on OLC.
  4. De Bruijn graph approach. Velvet, SPAdes, ABySS and other de Bruijn graph assemblers. Some theoretical constructions. Effective construction of de Bruijn graph.
  5. Repeats are bottleneck of de novo genome assembly. Repeat resolution algorithms. exSPAnder. Ray. Telescoper. Some theoretical constructions.
  6. Reference-assisted assembly.
  7. How can we deal with mammalian and plant size genomes? Minia, MaSuRCA, JR-Assembler. Some examples.
  8. Assembly of diploid genome. Inbreeding. Hapsembler, HaploMerger, dipSPAdes.
  9. Haplotype assembly. HapCUT, HapCompass, extensions for polyploid cases.
  10. Story of two genomes, Ciona savignyi and Ciona intestinalis: from sequencing to finishing.
  11. Assembly of metagenomics data.
  12. Reconstruction of ancestral genome.

Материалы курса