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All Projects → VascoElbrecht → Jamp

VascoElbrecht / Jamp

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JAMP - Just Another Metabarcoding Pipeline

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bioinformatics

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View All Similar Projects ➔

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.

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

JAMP is for non profit and accademic use only. If you wish to use JAMP comercially, please request permission from Vasco Elbrecht first. Thank you!

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("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")

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
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