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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
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
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.
- Please feel free to post a question on the Microbiome Helper google group if you have any issues.
- General comments or inquires about Microbiome Helper can be sent to morgan.langille@dal.ca.
Useful Links
Main SOPs
Amplicon SOP v2 (virtual box workflow)
Amplicon SOP v2 (qiime2-2022.11)
Amplicon SOP v2 (qiime2-2024.5)
PacBio Amplicon SOP v2 (qiime2-2022.2)
Tutorials
- CBW 2024 Workshops
- CBW-IMPACTT-workshop-tutorials-2023
- Intro to Unix
- ICG workshop tutorials 2023
- IMPACTT workshop tutorials 2022
- PICRUSt2 (CBW 2021)
- Metagenomics (CBW 2021)
- Intro to GNU Parallel
- BIOC4010 16S Tutorial
- Metagenomics Tutorial (Humann2 based)
- Download From SRA
- Random Forest Tutorial in R
- Other Tutorials