{"id":25437972,"url":"https://github.com/alexcoppe/bio-dockers","last_synced_at":"2026-03-18T02:33:22.228Z","repository":{"id":49791571,"uuid":"52302518","full_name":"alexcoppe/bio-dockers","owner":"alexcoppe","description":":whale: Bio-dockers: dockerized bioinformatic tools","archived":false,"fork":false,"pushed_at":"2025-01-10T13:55:24.000Z","size":911,"stargazers_count":32,"open_issues_count":1,"forks_count":9,"subscribers_count":7,"default_branch":"master","last_synced_at":"2025-01-10T14:37:00.188Z","etag":null,"topics":["bioinformatics","docker","genomics","ngs"],"latest_commit_sha":null,"homepage":"","language":"Dockerfile","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/alexcoppe.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2016-02-22T20:15:55.000Z","updated_at":"2025-01-10T13:55:28.000Z","dependencies_parsed_at":"2024-01-03T17:26:13.432Z","dependency_job_id":"bdd3e2c7-7dd5-4b56-bf5d-250318097d24","html_url":"https://github.com/alexcoppe/bio-dockers","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/alexcoppe%2Fbio-dockers","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/alexcoppe%2Fbio-dockers/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/alexcoppe%2Fbio-dockers/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/alexcoppe%2Fbio-dockers/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/alexcoppe","download_url":"https://codeload.github.com/alexcoppe/bio-dockers/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":239264765,"owners_count":19610060,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["bioinformatics","docker","genomics","ngs"],"created_at":"2025-02-17T09:28:22.155Z","updated_at":"2025-10-20T07:32:38.297Z","avatar_url":"https://github.com/alexcoppe.png","language":"Dockerfile","funding_links":[],"categories":[],"sub_categories":[],"readme":"# bio-dockers\n### :whale: Dockerized bioinformatic tools.\n\nA set of bioinformatics applications installed into a [Docker](https://www.docker.com) container, ready to be downloaded and used on any operating system \nsupported by [Docker](https://www.docker.com/).\n\nAll images are based on the [official Alpine Linux Docker image](https://hub.docker.com/_/alpine/) \nwhich is only 5 MB of size. The main goal is to obtain decently small portable bioinformatics software, easy to install and run.\n\nIn order to use a container on your computer, [install](https://docs.docker.com/engine/installation/) \nthe Docker daemon and check the links in the table \nbelow for instruction on how to pull the images from [Dockerhub](https://hub.docker.com/) and run them.\n\n| Program        | Description| Version | Image size |\n| ------------- |:-------------| :-------------| :-------------|\n| [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 |\n| [bedtools](https://github.com/alexcoppe/bio-dockers/tree/master/bedtools) |A powerful toolset for genome arithmetic| 2.31.1 | 166 MB |\n| [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 |\n| [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 |\n| [FastQC](https://github.com/alexcoppe/bio-dockers/tree/master/fastqc) | A quality control tool for high throughput sequence data | 0.11.7 | 235 MB |\n| [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 |\n| [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 |\n| [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 |\n| [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 |\n|[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 |\n| [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 |\n| [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 |\n|[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 |\n| [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 |\n| [SnpEff](https://github.com/alexcoppe/bio-dockers/tree/master/snpeff) | Genetic variant annotation and effect prediction toolbox | 4.3T | 353 MB |\n| [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 |\n| [Trimmomatic](https://github.com/alexcoppe/bio-dockers/tree/master/trimmomatic) | A flexible read trimming tool for Illumina NGS data | 0.39 | 172 MB |\n| [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 |\n| [VarScan](https://github.com/alexcoppe/bio-dockers/tree/master/varscan) | Variant detection in massively parallel sequencing data | 2.4.3 | 124 MB |\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Falexcoppe%2Fbio-dockers","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Falexcoppe%2Fbio-dockers","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Falexcoppe%2Fbio-dockers/lists"}