Two-part pipeline for processing 16S rRNA or ITS amplicon sequences specifically for the University of Maryland Baltimore Institute for Genome Sciences

part1.sh demultiplexes, filters, trims, and merges 16S or ITS paired-end reads. The script can be launched from any location on the IGS server according to this template:

part1.sh (-i <input directory> | -r1 <fwd reads> -r2 <rev reads> [-i1 <index 1> -i2 <index 2>]) -p <project> -r <run> -m <map> [-v <variable region>] [--1Step] [<options>]

Please run part1.sh --help for complete documentation.

Running part1.sh outside of IGS servers is not yet supported. It is possible however to modify hard-coded paths in part1.sh and illumina_dada2.pl to configure the pipeline for one's own running environment.

part2_illumina_dada2.pl runs the DADA2 ASV classification pipeline on one or more runs in the same project. On a RHEL7 IGS machine:

screen
qlogin -P jravel-lab -l mem_free=500M -q interactive.q
export LD_LIBRARY_PATH=/usr/local/packages/gcc/lib64
source /usr/local/packages/usepackage/share/usepackage/use.bsh
use python-2.7
use qiime
cd <project directory created by part1.sh>
part2_illumina_dada2.pl -i <comma-separated-input-run-names> -v <variable-region> -p <project-ID>

You can close the terminal at any time. To return to this process in another session, run: screen -r

Choose one of the following options.

-To create a local git clone:

git clone https://github.com/jbholm/IGS_dada2_pipeline.git

-To update your local git clone while discarding your local development history:

git fetch origin master
git reset --hard FETCH_HEAD

-To merge the changes into your local git clone:

git checkout master
git pull -X patience # Git may not be able to merge all the changes without manual editing

Find the desired version on https://github.com/jbholm/IGS_dada2_pipeline/commits/master. Click the "<>" button to browse the repository. Click the green "Clone or download" dropdown and click "Download ZIP" to download this version of the pipeline.

In a local clone:
Enter the following commands to save any existing changes to Git's stash and checkout a previous commit (change 1.0.0 to your desired version).
git add .
git stash # To discard changes instead of stashing them, git reset --hard
git rev-list master --grep='v1.0.0' | head -n 1 | xargs git checkout

To create a local clone:
Follow the desktop instructions above to find the desired version of the pipeline. Click the green "Clone or download" dropdown and copy the HTTPS URL. Then run: git clone PASTE/HTTPS/URL/HERE

The contents of taxonomy/silva/ are derived from the Silva database, and reformatted for DADA2 by Benjamin Callahan. They are available under the Silva dual-licensing model for academic and commercial users: https://www.arb-silva.de/silva-license-information/

This repository's copy of the UNITE database at taxonomy/sh_general_release_dynamic_01.12.2017.fasta is available under Attribution-ShareAlike (CC BY-SA).

All other files in this respository are available under GPLv3.