Week 1: practical metabarcoding

[rvosa]

As of commit f366c6becd25f0af492b1575633933efe48c887b there is now a set of gzipped FASTQ files that Jozsef Geml has made available for testing purposes. These are supposed to be processed, roughly, according to the steps outlined here. However, these steps are based on Jozsef's (windows-based) workflow. The general idea is that we translate these to a linux-based, open source workflow, that we can let the students run as a shell script.

What this means, specifically, is the following:

• The end result is a workflow shell script (with a lot of comments) that we will store in the same git repository folder as the data files. Another likely end result is a python (or other lang) script that does the sequence renaming (see below).
• Find a workaround in the workflow so we don't need Geneious. Jozsef uses Geneious to filter and trim sequences, we should be able to do this with FASTX-toolkit instead.
• Geneious is also used to do some sequence renaming, namely to add sample prefixes to the sequence identifiers (so the samples can subsequently be merged). It should be easy to script this in python or something.
• All the tools that I think we need (so, in addition to FASTX, those are mothur and usearch) are available on the virtual machine. Please do your work with that environment in mind and note if anything is missing.

[iadamo1]

Yesterday, I created the md file with all the steps revised during the meeting. I have sent it to Jòzsef in case he wants to make any changes or there is something that I missed. I am waiting for his reply to upload the final version.

[rvosa]

Perfect, thanks.

On Tue, Nov 21, 2017 at 11:25 AM, iadamo1 notifications@github.com wrote:

Yesterday, I created the md file with all the steps revised during the meeting. I have sent it to Jòzsef in case he wants to make any changes or there is something that I missed. I am waiting for his reply to upload the final version.

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