Shotgun Metagenomics Pipeline

Note:

Please use the latest version of the Snakemake pipeline maintained by GIS RPD team.

Description:

This pipeline is based on Bpipe, and is now routinely used by the group to process (pair-end) shotgun metagenomics samples.

Requirements:

• Bpipe 0.9.9 beta 1 (sge_fixes branch) or Snakemake 3.7.1
• MetaPhlAn 1.7.7 (http://huttenhower.sph.harvard.edu/metaphlan)
• Kraken 0.10.5 beta (https://ccb.jhu.edu/software/kraken/)
• BWA 0.7.10 (http://bio-bwa.sourceforge.net/)
• famas 0.0.10 (https://github.com/andreas-wilm/famas.git)
• HUMAnN 2 (https://bitbucket.org/biobakery/humann2/wiki/Home)
• Customized scipts:

• split_metaphlan_table.sh
• merge_tables.py (CSB5/misc_scripts/merge_tables.py)
• decont.py (CSB5/decont)

Usage:

• Using snakemake

$ snakemake_pipeline/create_config.sh FILE [FILE2 FILE3 ...]
$ snakemake_pipeline/run_pipeline.sh 

Note: You can modify the paths variables in the conf.yaml created by "create_config.sh".

• Using bpipe (this is no longer in use)

$ bpipe test -n200 run_metagenomics_pipeline.bpipe Sample_Folder1 <Sample_Folder2 Sample_Folder3 ...>
$ bpipe run -n200 run_metagenomics_pipeline.bpipe Sample_Folder1 <Sample_Folder2 Sample_Folder3 ...>