UNSW Genome Annotation Workshop

NOTE: Regrettably, this event has now been cancelled. We hope to organise something similar in future and will be in touch with registered individuals to gauge interest.

We are pleased to announce that we are hosting Monica Munoz-Torres from the Berkeley Bioinformatics Open-Source Projects group (BBOP) at Lawrence Berkeley National Laboratory as part of her EMBL-ABR Australian tour, sponsored by the School of Biotechnology and Biomolecular Sciences (BABS) and NSW Systems Biology Initiative (SBI).

In addition to a BABS seminar (details to follow), Monica will be giving a one-day Primer on Genome Annotation workshop at UNSW, with a particular emphasis on collaborative genome annotation using WebApollo.

• When: 0900-1700, July 7th, 2017
• Where: Red Centre, UNSW, Sydney, Australia
• Contact: richard.edwards@unsw.edu.au

You can pre-register for the workshop here or fill in the form below. Places are limited to 30 participants. We will be in touch to let you know if you have a place. Formal registration will require a $20 registration fee.

The SMRT way to sequence a yeast genome

Rich will be giving this week’s BABS School seminar (as part of a double header),

The SMRT way to sequence a yeast:
de novo genome sequencing and assembly with PacBio

Rountree Room Level 3
D26 Biological Sciences Building, UNSW
Friday 4 Sept 3.00pm

Abstract

We have performed PacBio single molecule real time (SMRT) sequencing of three yeast whole genomes. A haploid reference yeast strain (S288C) and two novel diploid strains were sequenced as part of a larger functional genomics project. For each strain, 2-2.6 Gb of usable sequence data was generated with read lengths of up to 53.3 kb. Pure PacBio whole genome de novo assemblies were generated using the HGAP3 pipeline. initial assembly of S288C yielded over 99.9% genome coverage at 99.997% accuracy with 15 of 17 reference chromosomes (16 nuclear chromosomes plus mitochondrion) essentially returned as a single, complete unitig. We are now using the S288C data to optimise the assembly process and derive assembly settings for the two novel strains. To this end, we have developed a new pipeline for the comparative assessment of high quality whole genomes against a reference. We are also exploring the trade-off between accuracy and sequencing depth of the PacBio “pre-assembly” and how this affects the final assembly.

[This work will also be presented at AGTA 2015, if you are interested and miss it.]