Consider updating the trimming tool to something a bit friendlier about wrangling-genomics

[sstevens2]

We also had a hard time with Trimmomatic in the lesson. It has a really long set of arguments which makes it so easy to make a mistake while typing. I moved running this into a script but we still had to troubleshoot a lot of errors that were related to typos. I've not used the other tools suggested by @JCSzamosi but if it could be swapped out, that would be ideal. Expect this change might be something that the CAC might need to discuss but I would be happy to help with a PR on it.

[harbi811]

I have used TrimGalore and found it a lot simpler to teach than Trimmomatic. TrimGalore is a wrapper around cutadapt and FastQC with the ability to detect common standard adaptors like Nextera used in the example. I am willing to contribute to rewriting this lesson using TrimGalore which would make the lesson easier to understand.

For example, there would be no need to copy a file of adapter sequences into the current working directory and the arguments are very descriptive. An equivalent command for the example using TrimGalore is. This also runs a FastQC step after trimming to check the quality of the trimmed reads. In that way, a person is able to see if the trimming was effective.

trim_galore --paired --phred33 --cores 4 --quality 20 --length 25 --nextera --fastqc SRR2589044_1.fastq.gz SRR2589044_2.fastq.gz

[JCSzamosi]

I'm not a maintainer on this lesson, but I sure would welcome a fork like that even if it never gets merged back into the Carpentries curriculum. If you do create such a fork, please let us know here!

Also thanks for the tip about TrimGalore! I will check it out for my own use!