I am Aswathi currently working in V1-V3 amplicon sequencing and analysis. I am doing my sequencing in illumina platform, and as it is not possible to sequence ~515 bp length V1-V3, I did a trial to make two libraries of the V1-V3 amplicon.
One PE library of 2X250 bp covering outer region of the amplicon and second one covering inner region of the same amplicon. Therefore, inner library R1 and R2 reads are overlapping and outer R1 and R2 lies far away. Then I tried to make a overlapped consensus amplicon sequences from these inner R1R2+Outer R1R2 merging together. I have used clustalO for the same. But I am able to produce very less (~5000) amplicon sequences using this methodology.
Can anyone suggest a better tool or approach for making amplicon from these two libraries?
Thank you. Aswathi