This is a curated collection of containers for bioinformatics, developed as part of the DNALinux project. It is based on the BioContainers project. All containers are hosted at Docker Hub.
Containers are grouped by category. Each name links to its directory, which contains the Dockerfile(s), available tags and usage notes.
- Data Access & Literature
- Sequence Processing & Quality Control
- Assembly, Scaffolding & Quality
- Alignment, Search & Variant Calling
- Annotation & Functional Genomics
- Comparative Genomics & Phylogenetics
- Specialized Omics & Imaging
- Utilities, Runtimes & AI Tools
- NCBI Datasets — Download genome sequences, annotations, and metadata from NCBI.
- SRA Toolkit — Download and convert sequencing data from the NCBI Sequence Read Archive.
- NCBI Tools (legacy) — Legacy NCBI text-based utilities and libraries.
- PaperJev — Retrieve PubMed papers, summarize PDF themes with local LLMs, and filter by relevance.
- FastQC — Quality control checks for high-throughput sequencing data.
- fastp — Ultra-fast FASTQ preprocessor for QC, filtering, and adapter trimming.
- Trimmomatic — Flexible read trimming for Illumina NGS data.
- PEAR — Memory-efficient paired-end read merger.
- Assemblers:
- Scaffolding & Finishing:
- 3D-DNA — Hi-C-based scaffolding and chromosome-length assembly.
- AllHiC — Hi-C scaffolding of contigs.
- Redundans — Scaffolding and reduction of heterozygous assemblies.
- SSPACE-LongRead — Long-read scaffolder for pre-assembled contigs.
- LR_Gapcloser — Close gaps in assemblies using long reads.
- gfatools — Manipulate GFA/rGFA assembly and pangenome graphs.
- Evaluation & Polishing:
- Aligners:
- Sequence Search:
- Variant Analysis:
- GATK — Variant discovery and genotyping framework.
- bcftools — Variant calling and VCF/BCF file manipulation.
- NanoCaller — Call SNPs and indels from long-read data.
- CADD — Score deleteriousness of human SNVs and indels.
- METAL — Meta-analysis of large-scale GWAS studies.
- Prokaryotic & Eukaryotic Annotation:
- Bakta — Rapid, standardized annotation of bacterial genomes, MAGs, and plasmids.
- Prokka — Rapid prokaryotic genome annotation.
- funannotate — Eukaryotic genome prediction, annotation, and comparison pipeline.
- EvidentialGene — Evidence-directed gene construction pipeline.
- Functional & Specialized Annotation:
- antiSMASH — Detection and analysis of secondary metabolite gene clusters.
- InterProScan — Scan protein sequences against InterPro databases.
- KofamScan — KEGG Orthology-based gene function annotation via HMMs.
- RepeatMasker — Screen DNA sequences for repeats and low-complexity regions.
- OrthoFinder — Infer orthogroups, gene trees, and rooted species trees.
- Clustal Omega — Accurate multiple sequence alignment of protein sequences.
- MUSCLE — High-throughput multiple sequence aligner.
- PHYLIP — Package of programs for inferring phylogenies.
- CVTree — Composition-vector-based phylogenetic tree construction.
- RSAT — Regulatory sequence analysis tools (motif discovery, TF binding).
- Metagenomics:
- Transcriptomics & Single-Cell:
- scRNA-seq R workflow — R environment for single-cell RNA-seq integration and clustering.
- BLAZE — Barcode identification from long reads for single-cell gene expression.
- Proteomics & Mass Spectrometry:
- Imaging & Browsers:
- Genomic Utilities:
- samtools — Process SAM, BAM, and CRAM alignment files.
- bedtools — Suite of utilities for feature manipulation and overlap analysis.
- bedGraphToBigWig — Convert bedGraph tracks to bigWig format.
- tabix — Generic indexer for TAB-delimited genomic position files.
- Jellyfish — Fast, memory-efficient k-mer counting.
- Primer3 — Design PCR primers and flanking oligonucleotides.
- Base Images & Libraries:
- biocontainers — Base image for BioDocker/BioContainers distributions.
- Python — Free-threaded Python builds (GIL-disabled).
- Biopython — Python library for computational biology.
- Dask — Library for parallel computing in Python.
- AI Applications:
- takollama — Local LLM integration and agentic AI application for biology (packaged with
uv).
- takollama — Local LLM integration and agentic AI application for biology (packaged with
The original BioContainers project contains many containers that are over five years old, with outdated bioinformatics software and based on older Linux versions. The goal of Omics Containers is to provide up-to-date software whenever possible, both at the operating system level and for bioinformatics tools. Additionally, it aims to make the containers compatible with multiple architectures when available.
You can use it from source and build a docker image. If you don't want to build the image yourself, you can pull it from Docker Hub. Once you have the image, you can run it to instanciate a container.
Go to the directory where the Dockerfile is, and run:
docker build -t name .
Search for the docker image you want in Docker Hub, select the version and run:
docker pull dnalinux/bwa
Each docker image has its own way to run it, see the overview section in DockerHub or the Dockerfile.
Open an issue in this repo telling which program you need.
Omics Containers is supported by DNALinux, Toyoko Bio, and a dedicated bioinformatics community.
Yes, every file in this repository is un the Apache 2.0 license, unless noted (some files comes with their own license). If you run these container in a cloud provider, they may charge you for the computer time needed to run the containers.
- Tonina — https://github.com/DNALinux/tonina
- DNALinux Docker Hub — https://hub.docker.com/u/dnalinux
- DNALinux — https://dnalinux.com/
- Toyoko Bio — https://toyoko.io/
- BioContainers — https://github.com/BioContainers/containers
If you have any feedback, please reach out to us at dnalinux@toyoko.io