README.md

PrimerTree

PrimerTree: Visually Assessing the Specificity and Informativeness of Primer Pairs

• Features
• Examples
• Installation
• Usage

Features

• Automatically query a primer pair and generate a tree of the products.
• Analysis can be run and then plotted in two commands.
• All options of Primer-Blast and clustal omega are supported.

Installation

R installation

CRAN

install.packages('primerTree')

Github

# install.packages("devtools")
devtools::install_github("jimhester/primerTree")

Clustal Omega Installation

Windows

Use the pre-compiled windows binary. Either put the installed clustalo.exe in your path, or pass the path to the executable in the clustal_options option

library(primerTree)
mammals_16S = search_primer_pair(name='Mammals 16S',
  'CGGTTGGGGTGACCTCGGA', 'GCTGTTATCCCTAGGGTAACT', clustal_options=c(exec='C:\Program Files\Clustal Omega\clustalo.exe'))

Linux

Simple installation from source

./configure && make && make install

If the resulting clustalo program is in your path it should be automatically found, otherwise see the windows instructions on how to specify the path to the executable.

Mac OSX

Clustal Omega can be installed from source but requires Xcode CLT and argtable, which are not pre-installed on OSX.

First install Xcode CLT.

xcode-select --install

then install argtable

brew install argtable

Now you can install Clustal Omega from source. From the clustalo directory:

./configure && sudo make install

Usage

Simple search for a Mammal 16S primer

library(primerTree)
mammals_16S = search_primer_pair(name='Mammals 16S', 'CGGTTGGGGTGACCTCGGA', 'GCTGTTATCCCTAGGGTAACT')
plot(mammals_16S)

Using the parallel features with the multicore package using the doMC backend, with 8 threads.

library(doMC)
registerDoMC(8)
library(primerTree)
mammals_16S = search_primer_pair(name='Mammals 16S',
  'CGGTTGGGGTGACCTCGGA', 'GCTGTTATCCCTAGGGTAACT', .parallel=T)
plot(mammals_16S)