Milí kolegové a kolegyně,
chtěli bychom vás srdečně pozvat na další přednášku semináře, která se koná tuto středu 22.11.2017, od 17:20 v posluchárně S4.
Hostem na semináři bude Andrew Page ze Sanger Institute, UK, a téma přednášky bude
High throughput pathogen informatics
Těšíme se srdečně na vaši účast!
Za všechny organizátory semináře s pozdravem, Petr Daněček
Stránky semináře http://bioinformatika.mff.cuni.cz/seminar/
--------------------------------------
High throughput pathogen informatics
The rapidly decreasing cost of sequencing has lead to an explosion in sequencing data. Over 300,000 samples have been sequenced and analysed by our Pathogen Informatics group, approximately 1/3 of all the sequenced pathogens in the world. The sheer volume of samples presents enormous computational and algorithmic challenges. Bioinformatics methods often do not scale in terms of time, memory or disk space. I will present a selection of recent bioinformatics analysis methods developed within Pathogen Informatics including:
1.) Gubbins can detect horizontal gene transfer in bacteria, producing a phylogenetic tree which is more representative of the actual underlying phylogeny, 2.) PlasmidTron can assemble the cause of phenotypes directly from raw NGS data, essentially GWAS for mobile genetic elements, 3.) ARIBA for detecting antimicrobial resistance genes using a hybrid assembly and mapping approach, 4.) SeroBA for serotyping Streptococcus pneumoniae, and 5.) Roary for building bacterial pan-genomes.
Andrew Page has a PhD in Computer Science in the area of scheduling in heterogeneous distributed systems. He has been the lead software developer in the Pathogen Informatics team at the Sanger Institute since 2011, developed over 30 open source software applications for bioinformatics, and has published 12 of them. He will shortly be moving to the Quadram Institute to take up the position of Head of Informatics.