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/

16S

• QIIME2

Trained QIIME2 taxonomic classifiers can be found here.

Metagenomics v3

• Bowtie2: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
• Bracken: https://ccb.jhu.edu/software/bracken/
• GNU Parallel (>= v20170322): https://www.gnu.org/software/parallel/
• KneadData: https://github.com/biobakery/kneaddata
• Kraken2: https://github.com/DerrickWood/kraken2/
• MMseqs2: https://github.com/soedinglab/MMseqs2
• PEAR: http://sco.h-its.org/exelixis/web/software/pear/doc.html
• PICRUSt2.0: https://github.com/picrust/picrust2/
• Trimmomatic: https://github.com/usadellab/Trimmomatic

Six compressed (pbz2) mapping files are required and must be placed in your working directory; they can be downloaded here here.

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

Old Metagenomics v1+v2

• Bowtie2: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
• DIAMOND (> v.0.7.0): https://github.com/bbuchfink/diamond
• GNU Parallel (>= v20170322): https://www.gnu.org/software/parallel/
• Human pre-indexed database: ftp://ftp.ccb.jhu.edu/pub/data/bowtie2_indexes/hg19.zip
• HUMAnN2: https://github.com/biobakery/humann
• MetaPhlAn2: https://github.com/biobakery/MetaPhlAn
• KneadData: https://github.com/biobakery/kneaddata
• PEAR: http://sco.h-its.org/exelixis/web/software/pear/doc.html
• Trimmomatic: https://github.com/usadellab/Trimmomatic

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.