Activity or Lab
This material introduces the AWS console interface, describes how to create an instance on AWS with the VMI provided and connect to that machine instance using the SSH protocol. Once connected, it requires the students to write a script to automate the tasks to create VCF files from two different sample genomes belonging to E.coli microorganisms by using the FASTA and FASTQ files in the input folder of the virtual machine. The same exercise can be applied if the VMI is installed on a local machine using virtualization software (e.g. Oracle VirtualBox). In this case, the Terminal program of the VMI can be used to do the exercise.
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Yildirim, Esma, "Designing Computational Biology Workflows with Perl - Part 2" (2019). CUNY Academic Works.