JAMP

Just Another Metabarcoding Pipeline - by Vasco Elbrecht - Twitter @luckylionde

JAMP is a modular metabarcoding pipeline, integrating different functions from USEARCH, VSEARCH, CUTADAPT and other programs. The pipeline is run as an R package and automatically generates the needed folders and summary statistics.

I am still working on the documentation, and the package is in beta thus if you run into issues or have questions please contact me per e-mail (luckylion07@googlemail.com).

For a a short tutorial on extracting haplotypes from metabarcoding datasets take a look at the denoising quick guide-Denoising-quick-guide!).

Initialling JAMP

Please keep in mind that JAMP needs Usearch, Vsearch, and Cutadapt installed to work properly. Thus Mac or linux based systems are recommended (and windows not officially supported!).

To install JAMP locally

# Installing dependencies needed fro JAMP
install.packages(c("bold", "XML", "seqinr", "devtools", "fastqcr"), dependencies=T)
# Load devtools and install package directly from GitHub
library("devtools")
install_github("VascoElbrecht/PrimerMiner", subdir="PrimerMiner")
install_github("VascoElbrecht/JAMP", subdir="JAMP")

You can also download the latest release of JAMP, extract and intal within R using install.packages("JAMP", repos = NULL, type="source")

Example of a system wide installation on a ubuntu|debian server:

wget https://github.com/VascoElbrecht/JAMP/archive/v0.53.tar.gz
tar -xzf v0.53.tar.gz
cd JAMP-0.53
sudo R CMD INSTALL JAMP