Metadata-Version: 2.1
Name: curatedmetagenomicspipeline
Version: 0.0.4
Summary: UNKNOWN
Home-page: https://github.com/waldronlab/curatedmetagenomics
Author: Francesco Beghini
Author-email: francesco.beghini@unitn.it
License: UNKNOWN
Description: ## 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`
        
Platform: UNKNOWN
Description-Content-Type: text/markdown
