This virtual training workshop is part of the Genetic Epidemiology and Bioinformatics Training Programme (GenEpi-BioTrain). It's organised by Statens Serum Institute (SSI), Denmark as part of Wave 2 dedicated to antimicrobial resistance (AMR).
The aim of this virtual training is to introduce participants to the software tools commonly used for assessing quality of and polishing Illumina and Nanopore bacterial sequencing data. The participants will gain insights into interpreting quality control (QC) parameters as well as how to handle bad quality reads and contaminated data.
Duration: Two half-days on 12 and 14 September 2023 from 09:00 to 12:30
Location: Online - Find the link after enrolment.
Audience: Microbiologists and bioinformaticians interested in quality assessment of sequence read data of bacteria. The training is targeted to those who are familiar with Unix command line interface.
Upon completion of this workshop, participants will be able to:
· Inspect rapidly the raw fastq files from the sequencer
· Understand how sequences can differ based on the preparation methodology
· Explain the differences between sequencing reads from Illumina and Nanopore
· Assess the quality of sequence data and trim bad reads
· Execute contamination control and clean contaminated data
· Generate an overview of the entire dataset using different tools
Participation: This course is open for public enrolment from 29 August to 12 September.