Can I perform de novo and reference chimera identification with chimera.uchime command

Hi everybody,

I’m following the MiSeq SOP of mothur wiki to process my 16S rDNA amplicon dataset (V4-V6 region).

I would like to identify and exclude chimeras from my dataset based on de novo and reference detection with uchime algorithm.

1st I used the command

chimera.uchime(fasta=sampleid.trim.contigs.good.unique.good.filter.unique.precluster.fasta, count=sampleid.trim.contigs.good.unique.good.filter.unique.precluster.count_table, dereplicate=t)

. This seems to identify as far as I know the chimeric sequences based on de novo detection method.

2nd I add the reference option of the same command

chimera.uchime(fasta=nice15.trim.contigs.good.unique.good.filter.unique.precluster.fasta, reference=silva.v4.v5.v6.fasta, dereplicate=t)

that seems to identify the reference chimeric sequences.

I would like to identify chimeric sequences based on both methods, because I believe that this are a big source of error regarding amplicon-based studies.

Can mothur's team members help me on this, please. Thanks in advance, @renh@

I would suggest only using the de novo approach. When you combine the two methods you significantly increase your risk of detecting false positives.


Thank you for your quick answer.