BOLD mtCOI database 2023-03-31 reformatted to SINTAX format for MB_Pipeline

Publicly available barcode records for the mitochondrial COI gene in the BOLD database (https://www.boldsystems.org/), release of 2023-03-31, reformatted to SINTAX format for the MB_Pipeline metabarcoding pipeline. The original data were released under a CC-BY-NC-SA license.

The conversion was performed with scripts from reformat-barcode-db (https://github.com/monagrland/reformat-barcode-db).  See log files for full command line and options used to filter sequences and prepare the HMMs. Different clustering, genetic code, and length parameters are required for each marker gene.

The Fasta files should be indexed to UDB format with Vsearch before use.

Description of files

All records:

bold.2023-03-31.coi-5p.all.fasta.gz - sequences in Fasta format, gzip compressed

bold.2023-03-31.coi-5p.all.log - log file for bold2sintax script

bold.2023-03-31.coi-5p.all.acc2bin - table of BIN identifiers for each accession, if available (else None)

European records only:

bold.2023-03-31.coi-5p.eur.fasta.gz - sequences in Fasta format, gzip compressed

bold.2023-03-31.coi-5p.eur.log - log file for bold2sintax script

european_countries.txt - List of country names used for subsetting

bold.2023-03-31.coi-5p.eur.acc2bin - table of BIN identifiers for each accession, if available (else None)

HMMer model for arthropod sequences:

bold.2023-03-31.coi-5p.arthropoda.hmm - HMM file

bold.2023-03-31.coi-5p.arthropoda.log - log file for bold2hmm script