recommended eukaryote 18S database?

Question

[gavinmdouglas]

Hey,

I'm interested in filtering out chimeric reads from 18S sequencing data using UCHIME (reference-based). However, the only eukaryote 18S database to use as a reference I can find is SILVA, which is much larger and not recommended by the UCHIME author. Are there other eukaryote 18S databases available which are of higher quality?

Thanks!

Gavin

[Chris Fields]

Interesting, did the UCHIME author mention why Silva isn't preferred? There aren't a lot of other options, I would expect they would recommend an alternative.

[gavinmdouglas]

The author discusses it here, apparently it contains "many low-quality sequences which degrade detection accuracy".

I should also say that only 16S and ITS sequences were tested with UCHIME so the author doesn't talk about 18S at all from what I can see. I don't see why the algorithm would be any worse for 18S sequences though.

[Chris Fields]

The impression I get from the QIIME and mothur users/devs is the opposite, that Silva is preferable over the others. See this link.

It may be a matter of filtering to remove the low-quality data; for example the versions of Silva SSU data for mothur are filtered to remove problematic sequences (see under 'Screening the sequences').

[gavinmdouglas]

Thanks for the info.