Requirements

The best way to use the Microbiome Helper SOPs is through our Virtual Box images since installing the required tools below may require substantial time and troubleshooting! However, if you do want to install the tools locally you'll need to download or clone our main GitHub repository (https://github.com/LangilleLab/microbiome_helper) if you want to use our scripts.

In addition, the following programs should be installed with commands accessible from the user's PATH, before trying to run any of the scripts included in this repository. These programs are required to run the main workflows, but there are many other tools available on our virtual box images.

Both pipelines

• FastQC (optional): http://www.bioinformatics.babraham.ac.uk/projects/fastqc/

Metagenomics

• Bowtie2: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
• DIAMOND (> v.0.7.0): http://ab.inf.uni-tuebingen.de/software/diamond/
• Human pre-indexed database: ftp://ftp.ccb.jhu.edu/pub/data/bowtie2_indexes/hg19.zip
• HUMAnN2: http://huttenhower.sph.harvard.edu/humann2
• GNU Parallel (>= v20170322): https://www.gnu.org/software/parallel/
• kneadData: https://bitbucket.org/biobakery/kneaddata/wiki/Home
• MetaPhlAn2: https://bitbucket.org/biobakery/metaphlan2
• PEAR: http://sco.h-its.org/exelixis/web/software/pear/doc.html
• Trimmomatic: http://www.usadellab.org/cms/?page=trimmomatic

The human (GRCh38) and PhiX bowtie2 index files can be downloaded here.

16S

• QIIME2

Trained QIIME2 taxonomic classifiers can be found here.

Visualization

• STAMP: http://kiwi.cs.dal.ca/Software/STAMP

Perl modules

File::Basename Getopt::Long List::Util Parallel::ForkManager Pod::Usage Sys::Cpu

If you're looking for earlier SOP database files, you can find them here.