spora: Streamlined Phylogenomic Outbreak Report Analysis
Project description
spora: Streamlined Phylogenomic Outbreak Report Analysis
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
Acknowledgments
Inspiration for code structure and design for spora was inspired by pangolin and civet, and minor code blocks were adopted from these software.
The Background section in the documentation describing outbreak definitions was written by Mark Horsman.
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