Summary and Help area for Week 2

In Week 2 we introduced you to the concepts of workflows and workflow management systems such as Nextflow. As the week progressed, we demonstrated how pipelines developed with Nextflow can perform the same types of tasks we outlined in Week 1 without you having to run each of the individual commands yourselves.

We showed you how to install Nextflow and introduced you to the viralrecon pipeline from the nf-core project. We then explained to you how to set up a samplesheet to be used as input for viralrecon and then got you to run the pipeline yourselves. Finally, we examined the outputs from viralrecon and explained how these could be used to decide whether the data we analysed was of sufficient quality for downstream analyses.

You also heard from a professional bioinformatician who uses Nextflow on a daily basis and how it has changed the way he approaches the analysis of large genomics datasets.

Do leave your comments about the learning in this week in the comments area below. In particular, did you learn anything that will be applicable to your own practice or study? Please share your thoughts with your fellow learners.

Looking forward to seeing you in Week 3!

Need help? In the comments section below, you can also leave any questions you might have about the Week 2 material and the educators and your fellow learners might be able to help.