trim.seqs on Illumina data?


Is it necessary to perform a trim.seqs on Illumina bacterial 16S rRNA data?

Contig was performed by the sequencing facility using FLASH software. We checked the quality score of the remaining sequences with the function “summary.qual(qfile=B3.qual)”. Our results showed an average quality score >30. Then raw sequences were selected based on the following criteria: (i) length (between 350 and 460 bp), (ii) homopolymer lengths (< 7) and (iii) the absence of ambiguous bases.

Thanks in advance for your reply.

No. In fact, it is strongly discouraged. Just use make.contigs and away you go…