Just Another Metabarcoding Pipeline - Twitter: @VascoElbrecht
JAMP is modular metabarcoding pipeline, integrating different functions from VSEARCH, CUTADAPT and other programs. The pipeline is run as an R package and automatically generates the needed folders and summary statistics for each processing step, allowing you to trouble shoot and adjust settings as needed. Checking the data and statistics after each processing step is a key element of JAMP and encouraged as it also gives you a better understanding of your data and the bioinformatic process.
End of 2021 update: Currently updating the documentation and older functions for a more streamlined experience 😄 .
For a a short tutorial on extracting haplotypes / ESVs from metabarcoding datasets take a look at the denoising quick guide-Denoising-quick-guide!).
Please keep in mind that JAMP needs Vsearch, and Cutadapt installed to work properly. Thus Mac or linux based systems are recommended (and windows not officially supported, but you can install e.g. a ubuntu shell on your windows system!).
# 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("tobiasgf/lulu")
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")
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 JAMPJAMP is for non profit and academic use only. If you wish to use any aspects of JAMP commercially, please kindly request permission from Vasco Elbrecht first. Thank you!