Question: BWA MEM Algorithm
1
gravatar for arunnatrajanravi
2.7 years ago by
France
arunnatrajanravi30 wrote:

Hi everyone,

I would like to understand how the algorithm behind BWA MEM works... So, I tried reading the papers on NCBI about BWA MEM and I even saw the posters about this but, I still can't understand completely how it works... Can someone explain it to me with some simple words?

Regards,

next-gen alignment • 7.3k views
ADD COMMENTlink modified 23 months ago by shivani9674520 • written 2.7 years ago by arunnatrajanravi30

How what works, exactly? The Burrows-Wheeler transformation? Mapping in general? BWA? The MEM algorithm?

ADD REPLYlink written 2.7 years ago by Brice Sarver2.4k

Thank you for your answer. Yes, I would like to know how it works in general. So, BWA Mapping in general and the MEM algorithm....

Regards

ADD REPLYlink written 2.7 years ago by arunnatrajanravi30
6
gravatar for mark.ziemann
2.7 years ago by
mark.ziemann1.0k
Australia/Mebourne/Monash University
mark.ziemann1.0k wrote:

Here's an intro to BWT for bioinformatics from Stanford Uni.

http://web.stanford.edu/class/cs262/presentations/lecture4.pdf

 

ADD COMMENTlink written 2.7 years ago by mark.ziemann1.0k
4
gravatar for vladimir.kovacevic
23 months ago by
Belgrade
vladimir.kovacevic50 wrote:

Hi!

I will risk to post the obsolete answer.

BWA execution from the high level can be observed as creating indexing structures (run bwa index which outputs 5 index files) out of sub-sequences of the reference genome (fasta file) in order to enable search of the sequence w from input reads (fastq format) in constant complexity - O(|w|). Indexing is based on the Burrows-Wheeler transformation (Google video with explanation of BWT and the interview with Mike Burrows https://youtu.be/4WRANhDiSHM?) and FM index https://en.wikipedia.org/wiki/FM-index.

After watching mentioned video and reading wiki you will be ready for the final treat, the BWA MEM paper from its author Heng Li: http://arxiv.org/abs/1303.3997

Hope this was helpful,
Vladimir Kovacevic

ADD COMMENTlink written 23 months ago by vladimir.kovacevic50
2
gravatar for arunnatrajanravi
2.6 years ago by
France
arunnatrajanravi30 wrote:

Hi Mark,

It doesn't explain BWA MEM algorithm. It sure helps to understand the basic concept BWA.

But I found this article:

http://arxiv.org/abs/1303.3997

I am not able to understand everypart of this paper.

Regards,

ADD COMMENTlink written 2.6 years ago by arunnatrajanravi30

What exactly do you don't understand?

ADD REPLYlink written 2.6 years ago by student-t420

Thank you for your question. I do understand the basic concept of BWA. But, What makes BWA-MEM very special because nowadays everyone is using it. And how it works? Can someone explain it to me with some simple words?

ADD REPLYlink written 2.6 years ago by arunnatrajanravi30
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