Virtual StatsPD@Waite meeting

Every month, the professional development meetings of statisticians and data scientists at Waite, known as StatsPD@Waite, bring together specialists in various aspects of data sciences in agriculture from Waite, Roseworthy and Adelaide.

Please join us for the next StatsPD@Waite seminar where Mario Fruzangohar and Julian Taylor from the Biometry Hub University of Adelaide will present on “Genome Sequence Analysis using novel tools and methods”.

Also please note that the StatsPD@Waite meetings are recorded. If you have a question to the speaker but had rather not be recorded, please send your question via chat during the meeting and it will be asked on your behalf.

Please email Beata Sznajder with questions or for details of the Zoom meeting.

Title: Genome Sequence Analysis using novel tools and methods

Presenter:Mario Fruzangohar and Julian Taylor, The Biometry Hub, University of Adelaide

In diploid organisms, whole genome haplotype assembly relies on the accurate identification and assignment of heterozygous single nucleotide polymorphism (SNP) alleles to the correct homologous chromosomes. This appropriate phasing of these alleles ensures combinations of SNPs on any chromosome, called haplotypes that is associated with important traits in organisms. In this research we present HaploMaker, a novel reference-based haplotype assembly algorithm capable of accurately and efficiently phasing long haplotypes using paired-end short reads and longer PacBio reads from diploid genomic sequences. To achieve this we frame the problem as a directed acyclic graph with edges weighted on read evidence and use efficient path traversal and minimization techniques to optimally phase haplotypes.

 Whole genome alignment of eukaryote species remains an important method for the determination of sequence and structural variations and can also be used to ascertain the representative non-redundant core genome sequence of a population. In this research we present CoreDetector, an easy-to-use general-purpose program that can align the core-genome sequences for a range of genome sizes and divergence levels.