Hi Every body.
I am using illumine hi-seq pair-end 100 strategy to sequence my V6 amplicons (20 barcode primers were utilized to encode sample information).
Now the problem is that, after joining paired reads into contigs
The contigs contained both “forward” and “reverse” sequence. Unlike 454, the pair reads seemed to be randomly sequenced in either direction in illumine hiseq.
I know mother have a simple command “reverse.seqs” to reverse compliment reads that are in reverse direction with 5->3 16S RNA gene.
But how to screen out the reverse contigs from large raw data.
Regards