mothur

I want to analyze amplicon metagenome data from PacBio platform

Dear colleague,
I use a Pacbio platform to generate full-length 16S amplicons data from environmental samples. I want to use Mothur to analyze the data. Could you advise me which database to use for the following steps:
sequence alignment
Chimaera
Classification
Thank you in advance for the support

Kind Regards

Hi Gilbert,

You’d use the same databases as we use with the MiSeq database. Of course, you’d need to customize the steps for full length sequences - namely, if align.seqs you’d use the full length rather than the V4 database.

Pat

Thank you for the prompt reply

Gilbert

1 Like