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 thatï¼Œ 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.