spora 0.6.5

spora: Streamlined Phylogenomic Outbreak Report Analysis

outbreaker

.. figure:: https://github.com/matt-sd-watson/outbreaker/actions/workflows/main.yml/badge.svg :alt: example workflow

example workflow

snakemake and Python integrated workflow for intermediate file generation for COVID outbreak analysis

Installation

::

git clone https://github.com/matt-sd-watson/outbreaker.git conda env create -f ncov_outbreaker/environments/environment.yml conda activate ncov_outbreaker cd outbreaker pip install .

Updating

::

conda activate ncov_outbreaker cd ~/outbreaker git checkout main git pull pip install .

Usage

::

usage: outbreaker -c <config.yaml> OR outbreaker --focal_list ...

Outbreaker: Python and snakemake outbreak workflow for COVID-19

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 outbreaker 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: 4 -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 outbreaker run. Default: Not enabled -v, --version Show the current outbreaker version then exit.

Documentation

More detailed documentation for outbreaker usage and functionality can be found here <docs/0-OVERVIEW.md>__

Acknowledgments

Inspiration for code structure and design for outbreaker 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.