https://github.com/alexcoppe/bio-dockers
:whale: Bio-dockers: dockerized bioinformatic tools
https://github.com/alexcoppe/bio-dockers
bioinformatics docker genomics ngs
Last synced: 12 days ago
JSON representation
:whale: Bio-dockers: dockerized bioinformatic tools
- Host: GitHub
- URL: https://github.com/alexcoppe/bio-dockers
- Owner: alexcoppe
- Created: 2016-02-22T20:15:55.000Z (over 9 years ago)
- Default Branch: master
- Last Pushed: 2025-01-10T13:55:24.000Z (10 months ago)
- Last Synced: 2025-01-10T14:37:00.188Z (10 months ago)
- Topics: bioinformatics, docker, genomics, ngs
- Language: Dockerfile
- Homepage:
- Size: 890 KB
- Stars: 32
- Watchers: 7
- Forks: 9
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
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README
# bio-dockers
### :whale: Dockerized bioinformatic tools.
A set of bioinformatics applications installed into a [Docker](https://www.docker.com) container, ready to be downloaded and used on any operating system
supported by [Docker](https://www.docker.com/).
All images are based on the [official Alpine Linux Docker image](https://hub.docker.com/_/alpine/)
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](https://docs.docker.com/engine/installation/)
the Docker daemon and check the links in the table
below for instruction on how to pull the images from [Dockerhub](https://hub.docker.com/) and run them.
| Program | Description| Version | Image size |
| ------------- |:-------------| :-------------| :-------------|
| [bamtools](https://github.com/alexcoppe/bio-dockers/tree/master/bamtools) |BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files.| 2.5.1 | 161 MB |
| [bedtools](https://github.com/alexcoppe/bio-dockers/tree/master/bedtools) |A powerful toolset for genome arithmetic| 2.31.1 | 166 MB |
| [Burrows-Wheeler Aligner](https://github.com/alexcoppe/bio-dockers/tree/master/bwa) |BWA is a software package for mapping low-divergent sequences against a large reference genome| 0.7.17 | 8.9 MB |
| [CIRCOS](https://github.com/alexcoppe/bio-dockers/tree/master/circos) |A software package for visualizing data in a circular layout | 0.69-9 | 182 MB |
| [FastQC](https://github.com/alexcoppe/bio-dockers/tree/master/fastqc) | A quality control tool for high throughput sequence data | 0.11.7 | 235 MB |
| [FASTX-Toolkit](https://github.com/alexcoppe/bio-dockers/tree/master/fastx-toolkit-lite) (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](https://github.com/alexcoppe/bio-dockers/tree/master/fastx-toolkit) | A collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing | 0.0.14 | 77.2 MB |
| [gatk 3](https://github.com/alexcoppe/bio-dockers/tree/master/gatk) | A variety of tools with a primary focus on variant discovery and genotyping | 3.7 | 289 MB |
| [GeneFuse](https://github.com/alexcoppe/bio-dockers/tree/master/genefuse) | A tool to detect and visualize target gene fusions by scanning FASTQ files directly. | 0.8.0 | 21.6 MB |
|[HISAT](https://github.com/alexcoppe/bio-dockers/tree/master/hisat2)| Graph-based alignment of next generation sequencing reads to a population of genomes | 2.2.1 | 391 MB |
| [MuTect](https://github.com/alexcoppe/bio-dockers/tree/master/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](https://github.com/alexcoppe/bio-dockers/tree/master/picard) | A set of command line tools for manipulating high-throughput sequencing (HTS) data and formats | 2.22.3 | 143 MB |
|[RNAsnp](https://github.com/alexcoppe/bio-dockers/tree/master/rnasnp)| Efficient detection of local RNA secondary structure changes induced by SNPs | 1.2 | 29.7MB |
| [Samtools](https://github.com/alexcoppe/bio-dockers/tree/master/samtools) | A suite of programs for interacting with high-throughput sequencing data | 1.17 | 33.1 MB |
| [SnpEff](https://github.com/alexcoppe/bio-dockers/tree/master/snpeff) | Genetic variant annotation and effect prediction toolbox | 4.3T | 353 MB |
| [SnpSift](https://github.com/alexcoppe/bio-dockers/tree/master/snpsift) | A toolbox that allows you to filter and manipulate annotated files | 4.3T | 353 MB |
| [Trimmomatic](https://github.com/alexcoppe/bio-dockers/tree/master/trimmomatic) | A flexible read trimming tool for Illumina NGS data | 0.39 | 172 MB |
| [VarDictJava](https://github.com/alexcoppe/bio-dockers/tree/master/vardict) | 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](https://github.com/alexcoppe/bio-dockers/tree/master/varscan) | Variant detection in massively parallel sequencing data | 2.4.3 | 124 MB |