Group 4 Genome assembly

When reading the information try to answer and discuss the following questions. Use these questions as a guideline to select information for your presentation.

a)    What are the main challenging factors in genome sequences, and in sequencing techniques, for the correct assembly of reads?

b)    Why are repetitive sequences and chimerisms so hard to assemble correctly?

c)     What is a problem with misassembly errors?

d)    What is the largest obstacle for chromosome scaffolding?

e)    How can long range sequence data be used to correct a deletion? And an insertion? And an inversion?

f)     Genome size, repeat content and heterozygosity are important factors for the resulting genome assembly quality. Why are these especially important in plants?

g)    Why can’t contigs be assembled into scaffolds without additional information?

h)    What is haplotype phasing? Why is this important in plants?

Piercing the dark matter, bioinformatics of long range sequencing and mapping, Sedlazeck et al., 2018.

The impact of third generation genomic technologies on plant genome assembly, Jiao et al, 2017.

Extra:

Do it yourself guide to genome assembly: https://academic.oup.com/bfg/article/15/1/1/1741842