The impact of linked reads technology in the de novo assembly of a large size genome: the olive fruit fly
Jiannis Ragoussis, PhD
Wednesday, November 29, 2017
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Chapters
Introduction
Olive cultivation around the world
Insecticide resistance
Olive fruit fly (Bactrocera oleae)
First pass denovo Genome Assembly uploaded in i5K
Application of linked read technology:
Assembly Process
Olive fly assembly mixing technologies, linked read advantage
Olive fly assembly mixing technologies, linked read advantage cont.
Technology combination evaluation: 10X Genomics-PacBio-Illumina MP
2. The combination of 10X with PacbIo dramatically reduces N bases in assembly
Olive fly Polytene chromosome map
Olive fly assembly mixing technologies, linked read advantage cont.
Better representation of repeats with 10X with or without addition of pacbio long reads
Reduction of genomic coordinates marked as unknown Mate pairs add gaps unrecoverable with PacBio
Number of splices aligned
Other species
Y- chromosome
Chromosome quotient: browser view of confirmed sequences
Y chromosome improvement
How many reads are needed?
Estimated fragment size
sampling by molecule vs per read
Olivefly sampling by molecule vs per read
Conclusions
Thank you
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