Add fasten and some of lskatz improvements

[boulund]

Continuation of #6

[boulund]

@lskatz As you mentioned elsewhere, fasten doesn't appear to remove any adapters at all? At least according to addadapters.sh from BBMap (which is getting quite old now as well and has been deprecated in BBMap I think). Not entirely sure why, but I haven't really looked into it.

I removed the random read generation, I didn't feel it was necessary. The small example FASTQ you pulled out of the larger one that was downloaded automatically before is great though! Keeping that in. I also added a small config file so potential users can choose whether to download a custom FASTQ or just do a quick test run with the small provided FASTQ.

I see there's something I need to fix with the Github action. I'll deal with that some other time.

[boulund]

I took care of the issues with the github action. Do you have any further questions, comments @lskatz ?

[lskatz]

Thank you for your time and your space on here! I am going to update to Fasten 0.8.7 where I updated the primer trimming in Fasten (it still does not have a great algorithm) but otherwise I agree with all changes!

[boulund]

I updated all tools to their latest versions:

• adapterremoval 2.4.3
• cutadapt 5.1
• fasten 0.8.7
• fastp 0.25.0
• trimmomatic 0.39 (unchanged)

Now it actually looks like fasten removes some of the adapters, so it appears the improvements you mentioned had an effect @lskatz !

[lskatz]

Now it actually looks like fasten removes some of the adapters, so it appears the improvements you mentioned had an effect @lskatz !

Thank you! Yes, it finally does something for that! This whole exercise got me to make the algorithm a bit better but I won't pretend that it is a great result as compared to the others. Thank you for you including my tool in the comparison!