I am new to bioinformatics and aim to get to show variety of 600 bp amplicon of an organism genome. I used two sets of primers each amplifying 415 bp of the 600 bp resulting in around ~200 bp overlapping region.

I pooled the amplicon of these two sets to become one sample and sent for sequencing.

Now I have a “R1” fastq.gz file and a “R2” fastq.gz file.

I plan my analysis to be

1. Merge PE reads of amplicon from each primer set
2. Assemble contig from the two merged amplicons
3. Show variety of sequence feature of contigs.

I tried around several things but not successfully got the result. Can I ask for the guidance?

Thank you so much