COInr a comprehensive, non-redundant COI database from NCBI-nt and BOLD
Description
COInr is a non-redundant, comprehensive database of COI sequences extracted from NCBI-nt and BOLD. It is not limited to a taxon, a gene region, or a taxonomic resolution. Sequences are dereplicated between databases and within taxa.
Each taxon has a unique taxonomic Identifier (taxID), fundamental to avoid ambiguous associations of homonyms and synonyms in the source database. TaxIDs form a coherent hierarchical system fully compatible with the NCBI taxIDs allowing creating their full or ranked linages.
COInr is a good starting point to create custom databases according to the users’ needs using mkCOInr scripts available at https://github.com/meglecz/mkCOInr
It is possible to select/eliminate sequences for a list of taxa, select a specific gene region, select for minimum taxonomic resolution, add new custom sequences, and format the database for BLAST, QIIME, RDP classifiers.
Notes
From COInr_2025_05_11 onward the selection of BOLD sequences is modified. Due to the relativelly frequent incorrectly labelled BOLD sequences among the ones lacking a BIN_URI, the following compromise has been adopted:
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For taxa that include other sequences with a BIN_URI, sequences without a BIN_URI are excluded from COInr.
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For taxa that only have sequences without a BIN_URI, those sequences are included in COInr.
Files
Files
(474.8 MB)
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Additional details
Related works
- Is cited by
- Software: https://github.com/meglecz/mkCOInr (URL)
- Is published in
- Preprint: 10.1101/2022.05.18.492423 (DOI)
- Journal article: 10.1111/1755-0998.13756 (DOI)