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for example we have two fragments. S1: ATCGTTGAGCAGACT and S2: TGAGCAGACTTAAGTAGTTTT they have an overlap zone"TGAGCAGACT". so the consensus is:ATCGTTGAGCAGACTTAAGTAGTTTT we sequenced this two fragments S1 and S2 in paired end reads R1 and R2. S1:R1: ATCGTTGAGCA S1:R2: AGTCTGCTCAA (illumina read the fragment in the other way so I think that to write in reverse complement. correct me if I'm wrong) S2:R1:TGAGCAGACTT S2:R2:AAAACTACTTA (reverse complement)I think this way is built the R2. how to make assembly in this case?
in both files (paired end), is what we must do the merging of the two files?
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