Reference database curation

Intro

This is the repository of the database curation pipeline for (meta-)barcoding for ITS2 vascular plants. Please cite the corresponding article: Quaresma, A., Ankenbrand, M.J., Garcia, C.A.Y. et al. Semi-automated sequence curation for reliable reference datasets in ITS2 vascular plant DNA (meta-)barcoding. Sci Data 11, 129 (2024). https://doi.org/10.1038/s41597-024-02962-5

Requirements

Compatible Database

These functions are intented for usage with databases that have a taxonomy stored in a specific format used for classifiers. Such databases can be created using BCdatabase: https://github.com/molbiodiv/bcdatabaser

Documentation: https://molbiodiv.github.io/bcdatabaser/

And particuarly syntax information: https://molbiodiv.github.io/bcdatabaser/output.html

Dependencies

Software dependencies are declared in bin/externals.txt These are

• Seqfilter: https://github.com/BioInf-Wuerzburg/SeqFilter
• NCBI eUtils Command line Tools: https://www.ncbi.nlm.nih.gov/books/NBK179288/
• VSEARCH: https://github.com/torognes/vsearch

Tested

This was tested under

• Mac OSX 11.0.1
• Ubuntu 20.04

Functions:

Automatized curation

1. Fungal removal
2. Non-target (non-ITS2) sequence removal
3. Removing incomplete taxonomies
4. Chlorophyta removal
5. Identify and remove iterative intra-spec outliers

(Details on these filters are provided in the article above)

This function performs the automated curation:

bash /bin/_curation.sh YOUR.DB.NAME.fa

Manual list curation by identified wrong NCBI taxonomies

• taxonomy corrections
• sequence removal

1. Place a .txt in the format as in the examples into the folder corrections. The format is

NCBI-Accession;Wrong_ScientificName;Corrected_ScientificName;Your_Name

Multiple separate files can be made, all .txt files in that folder will be used for corrections.

2. Then call the function on your database

bash /bin/_correct_manuals.sh YOUR.DB.NAME.fa

This can take a while for large databases.

Manual addition of sequences by patching taxonomy and inclusion

• adding taxonomy and appending to DB

1. Place one or more .fasta in the format as in the examples into the folder additions. The format is

>Scientific_name
ACGT

Multiple separate files can be made, all .fasta files in that folder will be used for additions.

2. Then call the function on your database

bash /bin/_add_manuals.sh YOUR.DB.NAME.fa

This can take a while for large number of sequences.

Subsetting: Input DB, list -> Output DB

Subsetting your input database into a geographically database

SeqFilter --ids_pattern LOCAL.FLORA.csv YOUR.DB.NAME.fa -o LOCAL.FLORA.DB.fa