Tutorial:Sequence Alignment from Scratch with BWA

Question

[barslmn]

Hi,

I made a step by step tutorial for initial BWA backtrack algorithm: https://omics.sbs/blog/bwa/bwa.html

Feedback and advice are most appreciated.

Edit: Updated on 16/12/2022

[Istvan Albert]

It is very impressive and helpful that you worked it all out in Python and explained it in great detail.

[Adeline]

Super nice tutorial, and like the others said cool that it's all done in Python and pretty detailed! I have a teensy remark though, the table with the output on the line with mapq: the 2^8 (to the power of) got copied into 28. And related to that, I would have loved a little more detail on the mapping quality mapq, but maybe that's for another post=) I also noted a couple of other little things, are you interested in proofreading comments as well?

[barslmn]

Thanks for pointing it out. I didn't look much into how the mapping quality is calculated, unfortunately. Every feedback is appreciated ^^.

[bestone]

Hello, I am working on the apricot. I will do an alignment to all data but I think that I need default parameters for alignment. Could you please help me with this issue?

[ATpoint]

You opened a question on this already. Please wait for responses. Don't spam other threads with unrelated comments. Thank you. By the way, the tool manuals are a great start, read them.

Answer 1

[Ram]

I really like the substance of your tutorial, but even as someone with 15+ years of bioinformatics and programming experience, it is sometimes difficult to follow the string transformations in the BWT section. Would it be difficult to break down that section further into sub-sections? For example, it looks like the suffix array part is a tangent, as you switch to what BWA does and there on out, the suffix array part is abandoned. You may want to add the SA part as a side note then, and explain what BWA does, then take a break at that point before jumping into recreating the original sequence from the last column.

Plus, I think you run into a language barrier of some sort at the reversible transformation part, as your explanation doesn't really make sense: you use the concept of "columns" as a foundational block but you haven't introduced columns at all until that point, and while trying to figure out what you mean by columns, I've lost track of all I've kept in mind about the BW transform so far. The end result is that I read and re-read until that point and then stop because I can't figure out what's going on.

[barslmn]

Thanks a lot, your comment is very insightful. My main goal when writing these to learn the topics myself. So any part that I can't explain well shows I need to improve my understanding of that part. I will be updating hopefully soon.