Seminars and Events

Past Events

Category Seminar
Date and Time 2015-04-17 14:00 - 15:00
Venue Auditorium C1F
Speaker Rei Kajitani
Affiliation School and Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology
Title Practical application of Platanus genome assembler
Poster click here to download(PDF)
Host Shigehiro Kuraku
Abstract Although it has been nearly a decade since the emergence of "high-throughput DNA sequencers," various protocols for de novo genome assembly exist and standardization have not yet been achieved. Currently, throughput of Illumina sequencers and quality of mate-pair (long-jumping) libraries continue to improve, and single-molecule sequencers are applied for de novo assembly, resulting in confusing circumstances to select a strategy.
In this seminar, I introduce the procedure to construct draft genomes, which utilized Illumina data and Platanus genome assembler (Kajitani et al. 2014). As its novel function, Platanus detects specific graph structures in the scaffolding step and merges highly heterozygous regions that include structural variants. In general, wild-type samples can be highly heterozygous, and it is expected to improve genome assembly for non-model organisms. In the original paper, the performance of Platanus was validated using benchmark data consisting of various species (nematode worms, oyster, bird, snake and fish). It was consequently adopted in the published genome projects: coelacanth (Nikaido et al. 2013), midge (Gusev et al. 2014) and three swallowtail butterflies (Cong et al. 2015; Nishikawa et al. 2015). Practically, the methods usually described in "supplementary materials," such as preprocess of reads and parameter setting in command lines, are influential for results, therefore I also focus on those procedures. With mate-pairs of which insert-sizes >10 kbp, our team has succeeded in achieving mega-order N50 lengths for eukaryotic genomes. Review of whole procedures of de novo assembly is helpful not only to improve the quality of draft genomes, but also to understand the progressing technologies related with genome projects.