FYRAflow is a snakemake based workflow for fission yeast species re-sequencing data analysis. \
- Overview of the
FYRAflow:
FastpKatBWASamtoolsPicard Tools(included in GATK4 packages)GATK4VcftoolsQUASTWhatshapLiftoffmaker(Please install it manually)EVidence Modeler(Please install it manually)R(Dependency for some GATK steps)
git clone https://github.com/guosongjia/FYRAflow.git
conda env create -n fyraflow -f env.yaml
conda activate fyraflow
# Please check the parameters, and adjust them according to your circumstance
# ================== Parameters for fyraflow variant sub-modules ==================
## Project Name
PROJECT: test
## Fission yeast species of re-sequencing analysis
SPECIES: S_octosporus # "S_pombe" or "S_octosporus" or "S_japonicus" or "S_versatilis" or "S_osmophilus" or "S_cryophilus"
## Input the path of fastq files
READSPATH: example/raw_reads
## Input the working directory
WORKPATH: example/
## Input the sample list file
SAMPLE: example/sample.list
## Input the final output directory
OUTPUTPATH: example/
python main.py -h
This is the main python script for Fission Yeast Re-sequencing Analysis workflow.
usage: python main.py <mode> --help
modes: variant, assembly
# Run "variant" submodule as an example
python main.py variant -h
usage: python main.py variant -s <running step> -l <PATH to store log files>
fyraflow variant mode options
positional arguments:
variant
optional arguments:
-h, --help show this help message and exit
-s STEP, --step STEP Input the step the workflow: qualityControl,
kmerFiltering, readsMapping_duplicatesMark,
gvcf_calling, jointCallingFiltering
-l LOG, --log LOG Input the path to save the running time log files.