ampvis_workflow_scripts

Scripts and notes to generate data for the shiny_ampvis application (http://albertsenlab.org/shinyampvis/)

REWORK_16S.V13.workflow_v4.1.sh

Orignial script: https://github.com/MadsAlbertsen/16S-analysis/blob/master/data.generation/16S.V13.workflow_v4.1.sh

• Run this script to generates the otu_table needed for the shiny_ampvis application

Before run this script

Make sure to have the following softwares (the download links are in the script):

• trimmomatic-0.36
• FLASH-1.2.11
• GitHub branch "16S-analysis/scripts/" (https://github.com/MadsAlbertsen/16S-analysis/tree/master/scripts)
• vsearch
• fasta_number script from http://drive5.com/python/python_scripts.tar.gz
• rdp_classifer
• QIIME

Replace 16S-analysis/scripts/uparse.to.otutable.pl script by:

• REWORK_uparse.to.otutable.pl (https://github.com/JeremieMG/ampvis_workflow_scripts)

Import your 16S data (paired_end fastq) in the main reposotory or change the directory.

Create/Modify the "samples" file as explained in the script.

Use this script on the server

Just run the following command:

qsub queue_script.sh

Informations about this queue script:

QIIME is not a module loaded on the server, it was installed from MiniConda. Remove the next commands if QIIME is working on a module:

source activate/deactivate qiime1

Another informations

• Make sure to get the right paths for each software
• Don't use their webserver, install shiny-ampvis on your own computer (version is different)
• Create a metadata file