IGS_dada2_pipeline

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

Pre-processing 16S or ITS paired-end reads:

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.

Classifying ASVs:

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

To use the lastest version of this pipeline:

Terminal

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

To use an earlier version of this pipeline:

Desktop

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.

Terminal

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

License

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.