Snakemake-workflow-dna-seq-short-read-blend-map

A Snakemake workflow (in progress) for mapping DNA PacBio sequencing data with BLEND.

This repository contains a Snakemake workflow designed to facilitate the analysis of NCBI single-ended Pac BIO SRA files using BLEND. The workflow is divided into three distinct Snakemake files, each handling specific tasks in the analysis pipeline.

Workflow Overview

1. Snakemake File 1: Download and Initial Processing

Downloads single-ended Pac BIO SRA files from NCBI using accessions specified in an accessions.txt file.
Converts SRA accessions to a python list using read_accessions.py
Converts SRA files to FASTQ format.
Performs quality control using FastQC and MultiQC.

2. Snakemake File 2: Trimming and Additional QC

Trims the FASTQ files to enhance data quality.
Performs FastQC and MultiQC on the trimmed files for post-trimming quality assessment.

3. Snakemake File 3: BLEND Indexing and Mapping

Indexes the reference genome for BLEND analysis.
Maps the preprocessed reads to the indexed reference genome using BLEND.
Converts SAM files to BAM format.
Utilizes Samtools to extract mapping statistics, including overall statistics (samtools stats) and flag statistics (samtools flagstat).

Usage

Prerequisites

Before running the workflow, ensure you have the necessary tools installed, such as fastqc, sra-tools, trimmomatic, samtools, and BLEND.

conda install -c bioconda snakemake
conda install -c bioconda fastqc trimmomatic samtools 
conda install -c bioconda blend-bio

For running the workflow:

Clone this repository:

git clone https://github.com/fulbelin/Snakemake-workflow-dna-seq-short-read-blend-map.git
cd Snakemake-workflow-dna-seq-short-read-blend-map

Prepare an accessions.txt file and trimmed_acessions txt file with the desired SRA accessions for download and trimming.

Execute the Snakemake files sequentially:

snakemake --snakefile Snakefile1 --cores 1 --latency-wait 30
snakemake --snakefile Snakefile2 --cores 1 --latency-wait 30
snakemake --snakefile Snakefile3 --cores 1 --latency-wait 30

Notes

Each Snakemake file is modular, allowing for independent execution or integration into other workflows.
Adjust the parameters in the Snakemake files according to your specific needs.
Feel free to customize and extend this workflow to suit your requirements. For detailed information on each step and the parameters used, refer to the respective Snakemake files and associated configuration files.
The wrapper was tested on SRR24768604 ERR10357101 IDs.

If you encounter issues or have suggestions for improvements, please open an issue in the repository. Happy analyzing!