I have some samples, where each has PE reads(150 bp length) of NGS in fastq format.
I already aligned them to the refseq with BWA.
I want to take N bases and do some kind of manipulation on them.
I thought to assemble the bam file, with the mutations, and in the gaps(where I don't have reads) fill it with the refseq.
do you know any reference-guided assembly that creates genomes to each sample, so I can take n bases from wherever I want?