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Thursday, August 3 • 10:00 - 10:20
Some components for assembling large genomes and metagenomes

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I will talk about the integration of some recent algorithms into software that address the challenges of large genomes and metagenomes de novo assembly. In particular, I will highlight (1) a minimal perfect hashing technique that is capable of indexing billions of elements quickly and in low memory, (2) an efficient unitig graph construction software (BCALM 2), and (3) recent developments in the Minia 3 assembler regarding multi-k contigs assembly that draw inspiration from the SPAdes assembler. These components are integrated into a software pipeline called Minia-pipeline, which recently provided high-ranking assemblies in the Critical Assessment of Metagenomic Interpretation challenge. References and software: Chikhi R et al, in preparation. https://github.com/GATB/gatb-minia-pipeline Rizk G et al, in submission. https://github.com/rizkg/BBHash Chikhi R et al, ISMB 2016. https://github.com/GATB/bcalm Sahlin et al, Bioinformatics 2016. https://github.com/ksahlin/BESST


Thursday August 3, 2017 10:00 - 10:20
Graduate School of Management Building, room 309 Volkhovskiy Pereulok, 3, St. Petersburg, Russia

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