ebdbcb/genome_alignment repository overview

Sequence reads alignment to a reference genome using BWA.

BWA, short for Burrows-Wheeler Aligner, is a popular bioinformatics tool used for mapping sequence reads to a reference genome. It employs the Burrows-Wheeler Transform (BWT) algorithm, which is highly efficient for aligning short sequencing reads to large reference genomes.

The current docker image is based on Ubuntu 22.04 and contains the following software:

• bwa v0.7.17 (https://github.com/lh3/bwa/releases/download/v0.7.17/bwa-0.7.17.tar.bz2⁠)
• gatk v3.7.0 (https://storage.googleapis.com/gatk-software/package-archive/gatk/GenomeAnalysisTK-3.7-0-gcfedb67.tar.bz2⁠)
• GenomeAnalysisTK 3.7.0 (https://storage.googleapis.com/gatk-software/package-archive/gatk/GenomeAnalysisTK-3.7-0-gcfedb67.tar.bz2⁠)
• miniconda (https://repo.anaconda.com/miniconda/Miniconda3-4.3.11-Linux-x86_64.sh⁠)
• picard v2.25.5 (https://github.com/broadinstitute/picard/releases/download/2.25.5/picard.jar⁠)
• samtools v1.9 (https://github.com/samtools/samtools/releases/download/1.9/samtools-1.9.tar.bz2⁠)

It requires to mount the folder containing the scripts and data as a volume when running the docker image locally:

docker run -it -v /path_to_your_data:/data genome_alignment /bin/bash

The Dockerfile used to build this image is available here: https://gitlab.com/ebd-bcb/dockerfiles/-/blob/master/dockerfile_genome_alignment⁠

More information at: https://gitlab.com/ebd-bcb/genome-alignment-using-bwa⁠

build by Raúl Ortega