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mkCOInr

★ 20 Open GitHub ↗

Make a non-redundant, comprehensive COI database from NCBI and BOLD and include customizing options

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# mkCOInr - COInr

**mkCOInr** is a series of Perl scripts that aims to **create and customize** **COInr**, a large, comprehensive, **COI database form NCBI-nucleotide and BOLD**.

The COInr database is composed of two files
 - COInr.tsv contains sequenceIDs, taxIDs, and sequences
 - taxonomy.tsv contains all taxIDs and associated information

**COInr** is freely available and can be easily downloaded at [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.6555985.svg)](https://doi.org/10.5281/zenodo.6555985)

## Documentation
The **[mkCOInr documentation](http://mkCOInr.readthedocs.org/)** is hosted at ReadTheDocs.

## COInr

- COInr is not specific to a particular region of the COI gene (sequences can be partial). 
 - All cellular organisms are included, even Bacteria. 
 - Sequences with incomplete lineages (e.g. assigned to a family without further precision) are present in the database
 - Taxa are taken into account only with correct latin name formats (e.g. instead of 'Proterorhinus sp. BOLD:EUFWF4948-19', the sequence is assigned to *Proterorhinus* genus without a species name)

The **database can be used directly for similarity-based taxonomic assignations** of metabarcoding data with any COI marker (primer pairs) of any geographical regions or target group.

Alternatively, the **database can be used as a starting point to create smaller, more specific custom databases**.

## mkCOInr

Sequences from COInr can be selected for :
 - A particular **gene region** (amplicon of a given primer pair)
 - **List of taxa** (sequences of a taxon list can be eiter selected or eliminated)
 - User-defined **minimal taxonomic resolution**

This can save a considerable amount of time and effort, since one of the most important challenges of creating a custom database is the mass downloading of the sequences and their pooling into a coherent taxonomic system.

**Custom sequences** can also be included and their taxonomic lineages is correctly handled.

COInr or the custom databases derived from it can be **formated to different database formats** (qiime, rdp, blast, vtam, full).

**Fig.1** The full pipeline to create COInr and options to make a custom database
![Fig1. Flowchart](https://raw.githubusercontent.com/meglecz/mkCOInr/main/doc/img/COInr_flowchart_readme.png)

## Major features of the creation of COInr

- Mass download of sequences and their taxonomic lineages from NCBI-nucleotide and BOLD databases
 - TaxIDs are used to avoid problems with homonyms and synonyms
 - Creation of a coherent taxID system. The hierarchical structure of the NCBI taxIDs is completed if necessary with new, negative taxIDs. 
 - When adding sequences with unknown taxIDs, taxon names are matched to already existing taxonomic lineages in the database to identify a correct existing taxID, or to assign a new one.
 - Taxonomically aware demultiplexing
 - Creation of a ready-to-use database in BLAST, RDP_classifier QIIME or a FULL tsv format

**Warning**
 - The taxonomic origin of the sequences is not checked, but taken as a face value from the source database. 
 - At the scale of the complete database I did not find a satisfactory method to blacklist sequences that are probably incorrectly assigned. However, if a small custom database is produced, the use of a phylogenetic method like SATIVA (https://github.com/amkozlov/sativa) becomes feasible and recommended to eliminate sequences of dubious origin.

## Citation

**Paper describing COInr and mkCOInr:**
Meglécz, E. (2023). COInr and mkCOInr: Building and customizing a non-redundant barcoding reference database from BOLD and NCBI using a semi-automated pipeline. [Molecular Ecology Resources, 21, 933-945](https://onlinelibrary.wiley.com/doi/10.1111/1755-0998.13756)

**COInr database:**
Meglécz, E. (2022). COInr a comprehensive, non-redundant COI database from NCBI-nt and BOLD [Data set]. [Zenodo](https://zenodo.org/records/6555985)

**mkCOInr:**  [github.com/meglecz/mkCOInr](https://github.com/meglecz/mkCOInr/tree/main)

mkCOInr

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