jibinjv/aligner repository overview

⁠Bioinformatics Aligner Docker Image

⁠Overview

This Docker image, jibinjv/aligner, is built from mambaorg/micromamba:1.5.0 and provides a comprehensive suite of bioinformatics tools for sequence alignment in next-generation sequencing (NGS) workflows. It uses Micromamba to manage a lightweight, efficient environment containing popular aligners. The image is optimized for size and performance by cleaning caches and stripping unnecessary files.

⁠Included Tools

The jibinjv/aligner image includes the following bioinformatics tools, installed via Conda channels conda-forge and bioconda:

• STAR⁠: Spliced Transcripts Alignment to a Reference
• HISAT2⁠: Fast and sensitive alignment for RNA-seq data
• GMAP⁠: Genomic mapping and alignment for mRNA and EST sequences
• TopHat2⁠: Spliced read mapper for RNA-seq
• Bowtie2⁠: Ultrafast short-read aligner
• Bowtie⁠: Original short-read aligner
• BWA⁠: Burrows-Wheeler Aligner for short and long reads
• BWA-MEME⁠: Memory-efficient BWA
• bwa-mem2⁠: Memory-efficient BWA ; ~1.3-3.1x faster
• Minimap2⁠: Versatile pairwise aligner for genomic and transcriptomic sequences
• NGMLR⁠: Long-read structural variant caller
• Salmon⁠: Transcript quantification from RNA-seq data
• Kallisto⁠: Near-optimal RNA-seq quantification
• Samtools⁠: Tools for manipulating SAM/BAM files

⁠Dockerfile Details

• Base Image: mambaorg/micromamba:1.5.0
• Environment: All tools are installed in a single Micromamba environment.

⁠Usage

⁠Pulling the Image

docker pull jibinjv/aligner:<tag>

⁠Running the Container

To start a container with an interactive shell:

docker run -it jibinjv/aligner:<tag>

To mount a local directory (e.g., /path/to/your/data) to the container's /data directory:

docker run -it -v /path/to/your/data:/data jibinjv/aligner:<tag>

To run a specific tool (e.g., STAR):

docker run -it jibinjv/aligner:<tag> STAR --version

⁠Example Workflow

1. Mount your data directory to /data.
2. Run the container and execute your bioinformatics pipeline using the installed tools. Example:

docker run -it -v /path/to/your/data:/data jibinjv/aligner:<tag> bash
STAR --runThreadN 4 --genomeDir /data/genome_index --readFilesIn /data/reads.fastq

⁠Notes

• Ensure sufficient disk space in the mounted /data directory for input/output files.
• Some tools (e.g., STAR, HISAT2) may require pre-built genome indices, which should be prepared and mounted into the container.
• For large datasets, allocate adequate memory and CPU resources to the container using Docker's resource flags (e.g., --memory, --cpus).
• The image is optimized for size, but performance may depend on the host system's resources.

docker build -t jibinjv/aligner:<tag> .

⁠License

This Docker image is licensed under the MIT License. Individual tools included in the image are subject to their respective licenses, as defined by their maintainers. Please refer to the documentation of each tool (linked above) for specific licensing information.

⁠Citation

If you use the jibinjv/aligner container, please cite the individual tools according to their publications.

Refer to the official documentation of each tool (linked above) for accurate citation and licensing details.

⁠Support

For issues or questions, please refer to the documentation of individual tools (linked above) or contact the repository maintainer.

⁠Maintainer

Jibin John⁠