No project description provided
Project 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
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
File details
Details for the file curatedmetagenomicspipeline-0.0.4.tar.gz.
File metadata
- Download URL: curatedmetagenomicspipeline-0.0.4.tar.gz
- Upload date:
- Size: 5.4 kB
- Tags: Source
- Uploaded using Trusted Publishing? No
- Uploaded via: twine/3.1.1 pkginfo/1.5.0.1 requests/2.22.0 setuptools/45.2.0.post20200209 requests-toolbelt/0.9.1 tqdm/4.42.1 CPython/3.7.6
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 | 0c1100ad5dcb1b90131e04ef4cf1562d8b146f30dd4879f3158564a83bd03757 |
|
| MD5 | 42a85b2b0d3d2ce8ce32a1a37ef6eeb7 |
|
| BLAKE2b-256 | 0ffad7b337a33286b221b6a9f0614cdb22922fb9389473d81bb4b6d9be39e66b |
