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Installation
From PyPi:
pip install curatedmetagenomicspipeline
From source code:
git clone git@github.com:waldronlab/curatedmetagenomics.git
cd python_pipeline
pip install .
Usage
cmd_pipeline --demo TEST_SAMPLE ERR262957 /output
The --demo argument causes use of a small demo FASTQ file and mini ChocoPhlAn, and UniRef databases (although ERR262957 is still downloaded to test fasterq-dump
cmd_pipeline MV_FEI4_t1Q14 "SRR4052038" /output
The command above download the specified SRR run for sample MV_FEI4_t1Q14 from the AsnicarF_2017 dataset. Reads are then processed for:
- Taxonomic profiling with MetaPhlAn 3.0
- Markers abundance and presence profiles are computed alongside the species-level profiling
- Strain-level profiling with StrainPhlAn 3.0 (only the consensus_marker step is done)
- Functional potential profiling with HUMAnN 3.0
- Pathways and gene families abundances are normalized using species' relative abundances and CPM
For the full list of options and commands, please run cmd_utilities_cli --help and/or cmd_utilities_cli COMMAND --help
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