FASTQ quality score to aligned sequence nucleotides

Question

[LG]

Hello biostars, Newbie here. I am trying to match-up/align the quality scores of a FASTQ to its aligned sequence.

Is there an aligner from which I can extract 'aligned' quality scores or has that information in its output?

If the raw sequence is put through an aligner that takes a FASTA (converted from original FASTQ, hence stripped of the quality scores ), is there a way to unify the quality scores from the raw FASTQ to its aligned nucleotide?

thx

[GenoMax]

If the raw sequence is put through an aligner that takes a FASTA

Curious why you would do that. Any specific reason? Taking Q-score away takes out important information that aligners use when they make alignment decisions.

is there a way to unify the quality scores from the raw FASTQ to its aligned nucleotide?

In what way? You have that information available in the original read.

[LG]

Hey genomax, thanks for your reply. I'm interested to do a small exploratory exercise to display the aligned sequence with their FASTQ quality score, to see how the different aligners are affected by this, and see how they relate to the quality metrics churned out by each aligner. The FASTA so I can do something like BLAST to add to the comparisons.

[GenoMax]

Make sure when you do the comparisons they are appropriate. BLAST does "local" alignments as its name says whereas most NGS aligners do global alignments.