BOLD systems database for qiime?

Question

[agata88]

Hi all!

Do you know if BOLD Systems database store files like mosquito_fasta and mosquito_taxonomy that can be used by QIIME?

Does NCBI database store information in required format for mosquito?

I would appreciate for help,

Best,

Agata

Answer 1

[Jon]

As far as I know, a QIIME compatible BOLD database for insects does not exist. I have created a subset of the BOLD databases for insects and chordates. The database is not perfect, but it was constructed using the unique BINs in the BOLD database to pull out "species". The database is compatible and distributed in my amplicon clustering software, which is called UFITS. It was originally developed for use in amplicon studies of fungal ITS regions, but we have recently gotten into COI based insect identification and thus it is now able to deal with ITS, LSU, 16S, and COI. UFITS is essentially a wrapper for a number of different tools/clustering algorithms (UPARSE, UNOISE2, DADA2, etc) and it is combined with taxonomy assignment as well. The output is then compatible with QIIME diversity scripts, PHINCH, PhyloSeq, etc. Of course I'm biased, but it is quite a bit easier to use then some other software solutions.

You can install UFITS using home-brew:

brew tap nextgenusfs/tap
brew update
brew install ufits

UFITS is available on github, and the README should have enough information to get you started, but on a typical laptop you should be able to process all of your data in a few hours. I would recommend the DADA2 "clustering" method for COI regions. Note that you will have to re-process your reads using UFITS as the QIIME processing scripts are not compatible. UFITS works best if you have the demultiplexed Illumina data from your sequencing center, i.e. paired end reads in a folder.