Feedback on Read Alignment Programs

[Mach2]

Hey everyone! I'm a microbiology undergrad in the middle of completing a work term with a bioinformatics team. My project for the semester involves researching different read alignment / mapping programs for the development of a future training course. One point that's been emphasized is that I should look into the effects of using the default parameters vs custom settings.

So far, I've been looking into Bowtie2, BWA and BWA-MEM, SMALT, segemehl, and BBMap. Reading the manuals and literature, trying to get a few test datasets, figuring out the different options for each program. I've also just added Minimap2 to my list, and will be reading up on that one over the coming days.

If you perform read alignments as part of your research, or have any other unique expertise on the subject, I'd be grateful for whatever insight you can offer! Here's an idea of the type of questions I'd like feedback on:

• What sequencing technology do you use to obtain your reads? What is your preferred tool for performing read alignments, and why? What advantage does it have over other available programs?
  
• Are there any unique challenges presented by the organisms you study or the sequencing technology you use? What adjustments do you make to your workflow to combat this?
  
• What factors do you place the most weight on when performing read alignments? Speed, adjustable parameters, low memory requirements?
  
• Do you use default settings, or custom options? If you use custom settings, what options do you change? Why is this necessary? How does it affect the outcome of your alignment?
  
• Any other info you think is valuable and would like to share with me!

Thanks in advance!