bold_identification

1 Introduction

see https://github.com/linzhi2013/bold_identification.

This is a Python3 package which can get the taxonomy information of sequences from BOLD http://www.boldsystems.org/index.php.

Currently, bold_identification only runs on Mac OS, Windows 64bit, Linux.

This script is part of the HIFI-barcode-SE400 pipeline (https://github.com/comery/HIFI-barcode-SE400).

2 Installation

Or with pip

$ pip install bold_identification

There will be a command bold_identification created under the same directory as your pip command.

3 Usage

run bold_identification

$ bold_identification
usage: bold_identification [-h] -i <str> [-f <str>] -o <str>
                            [-d {COX1,COX1_SPECIES,COX1_SPECIES_PUBLIC,COX1_L640bp,ITS,MATK_RBCL}] [-n <int>] [-r <int>]
                            [-c] [-C] [-q <int>] [-D] [--version]

To identify taxa of given sequences from BOLD (http://www.boldsystems.org/).
Some sequences can fail to get taxon information, which can be caused by
TimeoutException if your network to the BOLD server is bad.
Those sequences will be output in the file '*.TimeoutException.fasta'.

You can:
1) run another searching with the same command directly (but add -c option);
2) lengthen the time to wait for each query (-t option);
3) increase submission times (-r option) for a sequence.

Also, the sequences without BOLD matches will be output in the
file '*.NoBoldMatchError.fasta'

By Guanliang Meng.
See https://github.com/linzhi2013/bold_identification.

Citation:
Yang C, Zheng Y, Tan S, Meng G, et al.
Efficient COI barcoding using high throughput single-end 400 bp sequencing.
https://doi.org/10.1186/s12864-020-07255-w

version: 0.0.27

optional arguments:
  -h, --help            show this help message and exit
  -i <str>              input file name
  -f <str>              input file format [fasta]
  -o <str>              outfile prefix
  -d {COX1,COX1_SPECIES,COX1_SPECIES_PUBLIC,COX1_L640bp,ITS,MATK_RBCL}
                        database to search [COX1]
  -n <int>              how many first top hits will be output. [1]
  -r <int>              Maximum submission time for a sequence, useful for handling TimeOutException. [4]
  -c                    continuous mode, jump over the ones already in "-o" file, will resubmit all the remained. use "-cc"
                        to also jump over the ones in "*.NoBoldMatchError.fasta" file.
  -C                    For chimera check purpose. If set, for each sequence, I will query the BOLD database using the
                        subsequences from 5'- and 3'-ends with a length of '-q <int>' bp, respectively
  -q <int>              The length of subsequences for chimera check [400]
  -D                    debug mode output [False]
  --version             show program's version number and exit

4 Citation

When you use bold_identification in your study, please cite:

Yang C, Zheng Y, Tan S, Meng G, et al.
Efficient COI barcoding using high throughput single-end 400 bp sequencing.
https://doi.org/10.1186/s12864-020-07255-w

5 Publications which used this script

1. Arcila, Dahiana, et al. "Testing the utility of alternative metrics of branch support to address the ancient evolutionary radiation of tunas, stromateoids, and allies (Teleostei: Pelagiaria)." Systematic Biology 70.6 (2021): 1123-1144.

2. Huber, Bernhard A., et al. "Metagonia spiders of Galápagos: blind cave-dwellers and their epigean relatives (Araneae, Pholcidae)." Invertebrate Systematics 36.7 (2022): 647-678.

3. Klimova, Anastasia, et al. "Metabarcoding reveals seasonal and spatial patterns of arthropod community assemblages in two contrasting habitats: Desert and oasis of the Baja California Peninsula, Mexico." Diversity and Distributions (2023).

4. Huber, Bernhard A., and Guanliang Meng. "On the mysterious Seychellois endemic spider genus Cenemus (Araneae, Pholcidae)." Arthropod Systematics & Phylogeny 81 (2023): 179-200.