Data processing and visualization for metagenomics

Thu Jul 01 2021 at 09:00 am to Fri Jul 02 2021 at 05:00 pm

Online - day 1: https://uva-live.zoom.us/j/85083687937//// day 2: https://uva-live.zoom.us/j/81085815273 | Amsterdam

Marc Galland
Publisher/HostMarc Galland
Data processing and visualization for metagenomics This workshop is teach you how to carry out a common metagenomics workflow
About this Event

A lot of metagenomics analysis is done using command-line tools for three reasons:

1) You will often be working with a large number of files, and working through the command-line rather than through a graphical user interface (GUI) allows you to automate repetitive tasks.

2) You will often need more compute power than is available on your personal computer, and connecting to and interacting with remote computers requires a command-line interface.

3) You will often need to customize your analyses, and command-line tools often enable more customization than the corresponding GUI tools (if a GUI tool even exists).

In this workshop, you will be applying this new knowledge to carry out a common metagenomics workflow - identifying Operational Taxonomic Unities (OTUs) among samples taken from two metagenomes within a location. We will be starting with a set of sequenced reads (.fastq files), performing some quality control steps, assembly those reads into contigs, and ending by identifying and visualizing the OTUs among these samples.

A basic understanding of the command-line (e.g. Shell) is required for this course. You can self-study this Software Carpentry lesson for this.

Priority is given to employees of the SILS and IBED institutes (FNWI, UvA) and additional seats will be opened depending on the affluence.

This workshop is brought to you by the Amsterdam Science Park Study Group as part of the 2021 Summer School.


Event Venue & Nearby Stays

Online - day 1: https://uva-live.zoom.us/j/85083687937//// day 2: https://uva-live.zoom.us/j/81085815273, Online, Amsterdam, Netherlands

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