{"id":19909663,"url":"https://github.com/chrovis/duxhund","last_synced_at":"2026-02-13T09:58:35.470Z","repository":{"id":45567762,"uuid":"337966996","full_name":"chrovis/duxhund","owner":"chrovis","description":"DUX4 fusions finder","archived":false,"fork":false,"pushed_at":"2025-01-09T08:08:33.000Z","size":72,"stargazers_count":2,"open_issues_count":1,"forks_count":0,"subscribers_count":13,"default_branch":"main","last_synced_at":"2025-01-09T08:19:51.903Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Clojure","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/chrovis.png","metadata":{"files":{"readme":"README.md","changelog":"CHANGELOG.md","contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2021-02-11T08:14:18.000Z","updated_at":"2025-01-09T08:08:35.000Z","dependencies_parsed_at":"2023-01-22T07:47:18.704Z","dependency_job_id":null,"html_url":"https://github.com/chrovis/duxhund","commit_stats":null,"previous_names":[],"tags_count":4,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/chrovis%2Fduxhund","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/chrovis%2Fduxhund/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/chrovis%2Fduxhund/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/chrovis%2Fduxhund/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/chrovis","download_url":"https://codeload.github.com/chrovis/duxhund/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":233543384,"owners_count":18691801,"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":[],"created_at":"2024-11-12T21:16:18.277Z","updated_at":"2025-09-19T01:32:57.337Z","avatar_url":"https://github.com/chrovis.png","language":"Clojure","funding_links":[],"categories":[],"sub_categories":[],"readme":"# duxhund\n[![build](https://github.com/chrovis/duxhund/actions/workflows/build.yml/badge.svg)](https://github.com/chrovis/duxhund/actions/workflows/build.yml)\n[![test](https://github.com/chrovis/duxhund/actions/workflows/test.yml/badge.svg)](https://github.com/chrovis/duxhund/actions/workflows/test.yml)\n\nDUX4 fusions finder\n\n## Overview\n\nDuxhund is a dedicated tool to call DUX4 fusions.  It calls DUX4 fusions by the following three steps:\n- Align the input reads by BWA\n- Cut off softclips from the alignments and realign them with BWA, using a reference sequence that masks the pseudo-gene regions of DUX4\n- Extract appropriate triplets of alignments from the realigned result and call them with fusionfusion\n\n## Prerequisites\n### For running from the command line\n- [BWA](https://github.com/lh3/bwa)\n- [samtools](https://github.com/samtools/samtools)\n- [fusionfusion](https://github.com/Genomon-Project/fusionfusion)\n- Java JDK (\u003e= 8)\n- [Leiningen](https://leiningen.org/) (to build Clojure code)\n\n### For running in a Docker container\n- [Docker](https://www.docker.com/)\n\n## Usage\n\nDuxhund provides the following scripts:\n- `duxhund.sh`: to run from the command line\n- `duxhund_batch.sh` to run as an AWS Batch job\n\n### Running `duxhund.sh` script\n\nThe `duxhund.sh` script supports two ways to run:\n\n- To run in a Docker container\n- To run directly from the command line\n\n#### Running in Docker container\n\nTo run `duxhund.sh` in a Docker container, you'll need to build the Docker image first.\nTo build the Docker image, run:\n\n```sh\n./script/build.sh\n```\n\nOr, if you would like to name the resulting image, run:\n\n```sh\nIMAGE_NAME=\u003cimage name\u003e ./script/build.sh\n```\n\nBy default, the image name will be `chrovis/duxhund:latest`.\n\nOnce you build the image, you can run `duxhund.sh` as:\n\n```sh\ndocker run \u003cimage name\u003e duxhund.sh \u003carg\u003e ...\n```\n\n#### Running directly from command line\n\nTo run `duxhund.sh` directly from the command line, you'll need to build the Clojure code first.\nTo build it, run:\n\n```sh\nlein uberjar\n```\n\nAfter the Clojure code is successfully built, the `duxhund.jar` file will be generated in the `target` directory.\n\nTo run `duxhund.sh`, run:\n\n```sh\nDUXHUND_JAR=\u003cduxhund.jar path\u003e duxhund.sh \u003carg\u003e ...\n```\n\nIf you have the dependant tools (i.e. BWA, samtools and fusionfusion) installed not on your `PATH`, you'll need to specify their installation paths in addition:\n\n```sh\nBWA=\u003cbwa path\u003e SAMTOOLS=\u003csamtools path\u003e \\\nFUSIONFUSION=\u003cfusionfusion path\u003e DUXHUND_JAR=\u003cduxhund.jar path\u003e duxhund.sh \u003carg\u003e ...\n```\n\n### Options for `duxhund.sh`\n\nThe `duxhund.sh` script takes the following options as the command line arguments, which are all mandatory:\n\n- `--reference`: The path to the reference FASTA file\n- `--masked-reference`: The path to the masked reference FASTA file (see below for details)\n- `--target`: The path to the target BED file\n- `--r1`, `--r2`: The paths to the input FASTQ files\n- `--output`: The path to the output directory\n\n### How to make a masked reference\n\nA masked reference is a reference that is masked for the regions of DUX4 pseudo-genes.\nTo make a masked reference, run the following commands:\n\n```sh\n$ bedtools maskfasta \\\n  -fi \u003cinput FASTA file\u003e \\\n  -bed \u003cDUX4 pseudo-gene BED file\u003e \\\n  -fo \u003coutput FASTA file\u003e\n$ bwa index \u003coutput FASTA file\u003e\n```\n\nDuxhund bundles the DUX4 pseudo-gene BED file in the [`resources/`](resources) directory.\n\n## License\n\nCopyright © 2021 [Xcoo, Inc.](https://xcoo.jp/)\n\nThis program is distributed under the GNU General Public License v3. See [LICENSE](LICENSE) for details.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fchrovis%2Fduxhund","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fchrovis%2Fduxhund","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fchrovis%2Fduxhund/lists"}