curatedmetagenomicspipeline 0.0.4

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