FYRAflow: Fission Yeast Re-sequencing Analysis workflow

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Description

Guo-Song Jia@Li-Lin Du's lab

FYRAflow is a snakemake based workflow for fission yeast species re-sequencing data analysis. \

• Overview of the FYRAflow:

Full List of Tools used in this pipeline

• Fastp
• Kat
• BWA
• Samtools
• Picard Tools (included in GATK4 packages)
• GATK4
• Vcftools
• QUAST
• Whatshap
• Liftoff
• maker (Please install it manually)
• EVidence Modeler (Please install it manually)
• R (Dependency for some GATK steps)

Quick Start

Installation

Clone the repository:

git clone https://github.com/guosongjia/FYRAflow.git

Create the environment:

conda env create -n fyraflow -f env.yaml

Activate the environment:

conda activate fyraflow

Set up configuration file

Customize the workflow based on your need in config/*.yaml

Using config/variant_config.yaml as an example

# 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/

Run FYRAflow:

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.