The Role Of Alignment In Processing Sequencing Data

Question

[KCC]

I was reading that about MAQ and I found out that it does an alignment step. My understanding of MAQ is:

reads --> MAQ --> fastq

Then, with the fastq, we might commonly use an aligner next like BWA or bowtie:

fastq --> BWA --> SAM/BAM

I am sorry to be so rudimentary, but this is the state of my understanding so far. If MAQ is doing an alignment step, what's the goal of using an aligner right afterward?

Answer 1

[Michael]

Your understanding is wrong, MAQ has exactly the same purpose as BWA (Bowtie, BFAST, SHRiMP, etc) in such a workflow: fastq --> BWA/MAQ/... --> SAM/BAM