Metadata-Version: 2.1
Name: spora
Version: 0.7.0
Summary: spora: Streamlined Phylogenomic Outbreak Report Analysis
Home-page: https://github.com/matt-sd-watson/spora/
Author: Matthew Watson
Author-email: matthew.watson@oahpp.ca
License: UNKNOWN
Project-URL: Issues, https://github.com/matt-sd-watson/spora/issues
Project-URL: Source, https://github.com/matt-sd-watson/spora
Description: # spora: Streamlined Phylogenomic Outbreak Report Analysis
        
        ![example workflow](https://github.com/matt-sd-watson/spora/actions/workflows/main.yml/badge.svg)
        
        snakemake and Python integrated workflow for intermediate file generation for COVID outbreak analysis
        
        ## Installation
        
        ```
        git clone https://github.com/matt-sd-watson/spora.git
        conda env create -f ncov_spora/environments/environment.yml
        conda activate ncov_spora
        cd spora
        pip install . 
        ```
        
        ## Updating
        
        ```
        conda activate ncov_spora
        cd ~/spora
        git checkout main
        git pull
        pip install . 
        ```
        
        ## Usage
        ```
        usage: 
            	spora -c <config.yaml> 
            	OR
            	spora --focal_list ...<input args>
        
        spora: Streamlined Phylogenomic Outbreak Report Analysis
        
        optional arguments:
          -h, --help            Show the help output and exit.
          -c CONFIG, --config CONFIG
                                Input config file in yaml format, all command line arguments can be passed via the config file.
          -f FOCAL_SEQS, --focal-sequences FOCAL_SEQS
                                Input .txt list or multi-FASTA focal samples for outbreak. Required
          -b BACKGROUND_SEQS, --background-sequences BACKGROUND_SEQS
                                Optional input .txt list or multi-FASTA background samples to add to analysis
          -m MASTER_FASTA, --master-fasta MASTER_FASTA
                                Master FASTA of genomic sequences to select from. Required if either --focal-sequences or --background-sequences are not supplied in FASTA format
          -o OUTDIR, --output-directory OUTDIR
                                Path to the desired output directory. If none is provided, a new folder named spora will be created in the current directory
          -r REFERENCE, --reference REFERENCE
                                .gb file containing the desired COVID-19 reference sequence. Required
          -p PREFIX, --prefix PREFIX
                                Prefix string to label all output files. Default: outbreak
          -t NTHREADS, --nthreads NTHREADS
                                Number of threads to use for processing. Default: 2
          -s, --snps-only       Generate a snps-only FASTA from the input FASTA. Default: False
          -rn, --rename         Rename the FASTA headers to be compatible with NML standards. Default: False
          -nc NAMES_CSV, --names-csv NAMES_CSV
                                Use the contents of a CSV to rename the input FASTA. Requires the following column headers: original_name, new_name
          -ncs, --no-constant-sites
                                Do not enable constant sites to be used for SNPs only tree generation. Default: Enabled
          -fi, --filter         Filter both the focal and background sequences based on genome completeness and length. Default: Not enabled
          -gc GENOME_COMPLETENESS, --genome-completeness GENOME_COMPLETENESS
                                Integer for the minimum genome completeness percentage for filtering. Default: 90
          -gl GENOME_LENGTH, --genome-length GENOME_LENGTH
                                Integer for the minimum genome length for filtering. Default: 29500
          -rp, --report         Generate a summary output report for the spora run. Default: Not enabled
          -v, --version         Show the current spora version then exit.
        ```
        
        ## Documentation
        
        More detailed documentation for spora usage and functionality can be found [here](docs/0-OVERVIEW.md)
        
        ## Acknowledgments
        
        Inspiration for code structure and design for spora was inspired by [pangolin](https://github.com/cov-lineages/pangolin) and [civet](https://github.com/artic-network/civet), and minor code blocks were adopted from these software.
        
        The **Background** section in the documentation describing outbreak definitions was written by Mark Horsman. 
        
Platform: UNKNOWN
Description-Content-Type: text/markdown
