Fetching the assembled sequence from BWA aligned reads to reference genome

Question

[sharadlko1]

I am new to NGS analysis and started learning it. Recently, I aligned RAD PE reads to its reference genome using BWA for reference guided assembly of reads. Now my question is how I can fetch the assembled sequence. Please advise me!!

[lieven.sterck]

what have you tried so far (except aligning reads)? have you been reading up on this topic?

or google "reference guided assembly of PE reads" or such, that will give you already some indication. One of the first hits: https://www.researchgate.net/figure/Assembling-RAD-alleles-and-creating-RAD-contigs-from-RAD-paired-end-reads-Inset-Each_fig1_51097103