A set of bioinformatics applications installed into a Docker container, ready to be downloaded and used on any operating system supported by Docker.
All images are based on the official Alpine Linux Docker image which is only 5 MB of size. The main goal is to obtain decently small portable bioinformatics software, easy to install and run.
In order to use a container on your computer, install the Docker daemon and check the links in the table below for instruction on how to pull the images from Dockerhub and run them.
| Program | Description | Version | Image size |
|---|---|---|---|
| bamtools | BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files. | 2.5.1 | 161 MB |
| bedtools | A powerful toolset for genome arithmetic | 2.31.1 | 166 MB |
| Burrows-Wheeler Aligner | BWA is a software package for mapping low-divergent sequences against a large reference genome | 0.7.17 | 8.9 MB |
| CIRCOS | A software package for visualizing data in a circular layout | 0.69-9 | 182 MB |
| FastQC | A quality control tool for high throughput sequence data | 0.11.7 | 235 MB |
| FASTX-Toolkit (lite) | A collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing (lite version: no graphic commands) | 0.0.14 | 12.6 MB |
| FASTX-Toolkit | A collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing | 0.0.14 | 77.2 MB |
| gatk 3 | A variety of tools with a primary focus on variant discovery and genotyping | 3.7 | 289 MB |
| GeneFuse | A tool to detect and visualize target gene fusions by scanning FASTQ files directly. | 0.8.0 | 21.6 MB |
| HISAT | Graph-based alignment of next generation sequencing reads to a population of genomes | 2.2.1 | 391 MB |
| MuTect | A method for the reliable and accurate identification of somatic point mutations in next generation sequencing data of cancer genomes | 1.1.5 | 134 MB |
| Picard | A set of command line tools for manipulating high-throughput sequencing (HTS) data and formats | 2.22.3 | 143 MB |
| RNAsnp | Efficient detection of local RNA secondary structure changes induced by SNPs | 1.2 | 29.7MB |
| Samtools | A suite of programs for interacting with high-throughput sequencing data | 1.17 | 33.1 MB |
| SnpEff | Genetic variant annotation and effect prediction toolbox | 4.3T | 353 MB |
| SnpSift | A toolbox that allows you to filter and manipulate annotated files | 4.3T | 353 MB |
| Trimmomatic | A flexible read trimming tool for Illumina NGS data | 0.39 | 172 MB |
| VarDictJava | A variant discovery program written in Java and Perl. It is a partial Java port of VarDict variant caller | 1.5.1 | 631 MB |
| VarScan | Variant detection in massively parallel sequencing data | 2.4.3 | 124 MB |