BVCN Conference Tutorials and Examples
In June 2021, the BVCN hosted a virtual bioinformatics conference - Holistic Bioinformatic Approaches used in Microbiome Research - each of the six presenters were asked create an accompanying demo of the Featured Presentations.
As part of Dr. Martin Steinegger's presentation during the BVCN Conference in 2021 - "Metagenomic pathogen detection using MMseqs2, Plass, and Linclust" - Dr. Steinegger created a Python notebook that could be used as a companion tutorial for the presentation.
The presentation is hosted on our YouTube page
The companion tutorial can be launched using the button below. Once loaded, double-click the file BVCN.ipynb to get started.
Note #1: Launching Binder can take 10+ minutes.
Note #2: This Binder launches with both mmseqs2 and plass installed, so that step will be skipped. All other steps (database downloads, etc.) will happen as part of the tutorial and may take additional time (as compared to the presentation) due to the data limitations within Binder.
During her presentation - "Galaxy for microbiome via ASaiM story - From a local project to a global effort" (see YouTube video) - at the BVCN Conference in 2021, Dr. Batut mentioned a tutorial for Metatranscriptomics analysis using microbiome RNA-seq data on Galaxy.
The tutorial can be found online:
The tutorial can be run on the European Galaxy server (usegalaxy.eu).
During his talk at the 2021 BVCN Conference - "Tweedieverse - A single home for microbiome multi-omics differential analysis" (see YouTube video) - Dr. Mallick mentioned three complementary tools related to differential abundance analysis and synthetic benchmarking.
The corresponding tutorials can be found online:
Among these, the Tweedieverse tutorial is Binder-compatible and can be launched using the button below.
Note: Launching Binder can take a few minutes. Once loaded, double-click the Tweedieverse_microbiome.Rmd file in the R/ directory and click the Knit button to get started.
The companion slides can be downloaded from here.