PrimerMiner

PrimerMiner is a R based batch sequence downloader to design and verify metabarcoding primers. Sequences for a specified marker (e.g. COI) are obtained from NCBI and BOLD and clustered into Operational taxonomic units (OTU) to reduce bias introduced by over represented sequences in the data bases.

PrimerMiner requires an internet connection for downloading sequences and was only tested on MacOSX (should work on linux as well).

Documentation and video tutorials

Please take a look at the PrimerMiner wiki for detailed package documentation and tutorials. We are happy to help should you run into any issues or run into problems (contact: luckylion07@googlemail.com).

Quick guide

1. Installation You can install PrimerMiner directly from GitHub. You will also need to install BOLDconnectR.

install.packages("devtools")
library("devtools")
install_github("boldsystems-central/BOLDconnectR")
install_github("VascoElbrecht/PrimerMiner", subdir="PrimerMiner")

Alternatively, you can download a specific PrimerMiner version manually and install it with: install.packages("path_to_package_file", repos = NULL, type="source", dependencies=T)

Load the package with library("PrimerMiner"). You find all the commands and an executable example in the Sample_Data!

Important: you will need the apikey from you BOLD login to download bold data. You can find it under user settings in your BOLD login.

2. Batch downloading sequences Generate the configuration file by runing batch_config("config.txt")in R. Edit this file to review and change the default settings. Create a csv table containing the groups (and their subgroups if you want to download a subset of that group) for which data should be downloaded. See "taxa_small.csv" in the folder Sample_Data.

3. Batch download sequence data To start the batch download, run batch_download("taxa_small.csv", "config.txt") giving the name of the taxon table and configuration file.

4. Bild alignments Align OTUs and extract region interesting for primer development e.g. with Geneious and MAFFT. Export the aligned sequences as a fasta file. You can apply selective trimming on the edges to remove primer sequences from the alignment as well as remove gaps from the alignemnt with the selectivetrim() function.

5. Visualise alignments With plot_alignments(path_to_fasta_alignment_files) you can produce plots of the alignments, to use for primer design and visualisation (see Poster_introduction.pdf for an example).

6. In silico Primer evaluations are now available, see the wiki for more information.

Citation for this package

Elbrecht & Leese (2016). PrimerMiner: an R package for development and in silico validation of DNA metabarcoding primers - Methods in Ecology and Evolution

Contact

Vasco Elbrecht - luckylion07@googlemail.com