mothur

Assessing error rate with a mock community - 10 species (including fungi) in log distribution

Hello! I have used the ZymoBIOMICS Microbial Community Standard II as my mock community for a recent MiSeq run. I am stuck at seq.error
The command requires a reference FASTA and Zymo provides individual 16S&18S rRNA sequences (FASTA format) and genomes (FASTA format) for each strain. Do I need to combine those files to make one reference file or can I somehow include multiple references?

This is the provided instruction manual for that particular community: https://files.zymoresearch.com/protocols/d6310_zymobiomics_microbial_community_standard_ii(log_distribution).pdf

Thank you!

You don’t need the genomes, only the 16S rRNA gene sequences. You will want the sequences for all of the operons since they’re not identical within an organism.

Also, FWIW and for next time, I discourage the use of the log abundance community since your error rate will be driven by the most abundant organism. It’s really best to use the uniform abundance mock community.

Pat

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