Multiple Mappings to BAM

Description

This project is part of the Google Summer of Code 2024 program. It provides a Nextflow-based pipeline for processing DNA sequences and generating BAM files. The pipeline supports multiple mapping tools and various configurations to suit different research needs.

Features

• Supports multiple mapping programs (e.g., BWA, SMALT, SSAHA)
• Handles paired-end and single-end reads
• Quality filtering and duplicate marking
• Generates pseudosequences
• Supports indel calling and variant detection
• Configurable parameters for advanced usage

Installation

To install the necessary dependencies, ensure you have Nextflow installed. You can refer to the Nextflow installation guide for detailed instructions.

curl -s https://get.nextflow.io | bash

Additionally, you need to install Docker or Singularity. Follow the respective installation guides:

Docker Installation Guide
Singularity Installation Guide

Usage

Clone the repository and navigate to the project directory:

git clone
cd multiple-mappings-to-bam

Using the input CLI

Use the input CLI to pass the parameters. Run the CLI:

nextflow run main.nf --ref absolute/path/to/ref/file --program BWA --read_dir <path/to/directory/containing/reads>

Directly running the pipeline

The pipeline can be run without having to directly clone this code repository, using the following syntax (will execute the latest pipeline version):

nextflow run sanger-pathogens/Multiple-mappings-to-bam --ref absolute/path/to/ref/file --program BWA --read_dir <path/to/directory/containing/reads>

The outputs would be generated in the directory specified by the outdir param (default results/)