SLIM | A web app for environmental DNA metabarcoding analysis

What is it?

This project has been initiated by the Pawlowski group at the University of Geneva, Switzerland. Its aim is to bring easy access to state-of-art bioinfirmatic tools to non-specialist and/or to command-line reluctant for the processing of raw amplicon sequencing data, i.e. DNA metabarcoding, from illumina paired-end FASTQ to an annotated OTU matrix.

SLIM is a node.js web application providing a Graphical User Interface (GUI) to interact with bioinformatic softwares. It simplifies the creation and deployment of a processing pipeline and is accessible within an internet browser over the internet. It is maintained by Yoann Dufresne and Tristan Cordier.

The full documentation is available here, and on the WIKI

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Can I try it?

Yes! This website is intended to give you a demo of the tool’s possibilities. The demo server has a reduced processing capacity and the upload is limited to 2 Gb per file. This should be enough to process a full illumina MiSeq run.

To try it, you can either :

download this exemple tutorial to check by yourself the files and their required format.

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The SLIM demo server is » [HERE] « :( The server is down until further notice :(

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You are welcome to:

make suggestions and report bugs here
send a pull request here

Citation

Dufresne, Y., Lejzerowicz, F., Apotheloz Perret-Gentil, L., Pawlowski, J., & Cordier, T. (2019). SLIM : a flexible web application for the reproducible processing of environmental DNA metabarcoding data. BMC Bioinformatics, 20(1), 88. https://doi.org/10.1186/s12859-019-2663-2

Version history

v0.6

BUGFIX: resolved issues with the order of module execution when DADA2 is used. BUGFIX: resolved issues with the pipeline.conf file that did not included the checkbox and radio buttons.

v0.5.3

DTD: added an option for trimming the primers at the end of the reads in (for fully overlapping pair-end reads) and a contig length filtering

v0.5.2

DADA2 beta integration, small fix on IDATAXA

v0.5.1

BUGFIX of the IDTAXA module, added wiki for the module

v0.5

Integration of the IDTAXA module

v0.4.1

Fixed the Dockerfile to fetch the latest R version and CASPER util.c file

v0.4

Added timing checkpoints in the logs of the scheduler; Added the third-party software version infos in the email

v0.3

Fixed LULU module and the otu table writing is now done by a python script

v0.2

Updated the get_dependencies script.

v0.1

First release, with third-parties versions handled within the get_dependencies_slim.sh script.