recommended eukaryote 18S database?
0
0
Entering edit mode
6.0 years ago

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

 

 

 

chimera microbiome NGS • 3.5k views
ADD COMMENT
1
Entering edit mode

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.

ADD REPLY
0
Entering edit mode

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.

ADD REPLY
2
Entering edit mode

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').

ADD REPLY
0
Entering edit mode

Thanks for the info.

ADD REPLY

Login before adding your answer.

Traffic: 2484 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6