Sequence a genome II

Published in University of Lausanne, Department of Ecology & Evolution, 2016

This class is a genomics project and therefore it’s a different every year. I have participated in this class in years 2016 and 2017.

2016: Students extract RNA in four different conditions for an RNA-seq experiment on the bacterial strains they sequenced last semester. Students do a quality control of reads, trimming and pseudo-mapping reads to calculate transcript abundances and perform a downstream analysis using R with emphasis on genes they have annotated last semester.

2017: Comparative genomics. We have seuqenced bunch of lactobacilus strains from honeybees and bumblebees guts. Students in my working group were evaluating horizontal gene transfer events that happened after separation of bumplebee and honeybee clades, but before the radiation of strains we had sequenced.

All the materials I have created or co-created for all the years are available at GitHub.

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