{"id":22155929,"url":"https://github.com/citiususc/flinkbwa","last_synced_at":"2025-07-30T13:10:10.930Z","repository":{"id":68812633,"uuid":"95536482","full_name":"citiususc/FlinkBWA","owner":"citiususc","description":"FlinkBWA is a new tool that exploits the capabilities of a Big Data technology as Apache Flink to boost the performance of one of the most widely adopted sequence aligner, the Burrows-Wheeler Aligner (BWA).","archived":false,"fork":false,"pushed_at":"2017-07-13T10:44:56.000Z","size":1400,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":4,"default_branch":"master","last_synced_at":"2025-03-24T14:35:08.624Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"C","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/citiususc.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","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":"2017-06-27T08:37:55.000Z","updated_at":"2017-07-10T12:24:39.000Z","dependencies_parsed_at":null,"dependency_job_id":"81103b78-8e62-4dee-99a7-0145b1f34978","html_url":"https://github.com/citiususc/FlinkBWA","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/citiususc/FlinkBWA","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/citiususc%2FFlinkBWA","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/citiususc%2FFlinkBWA/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/citiususc%2FFlinkBWA/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/citiususc%2FFlinkBWA/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/citiususc","download_url":"https://codeload.github.com/citiususc/FlinkBWA/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/citiususc%2FFlinkBWA/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":267874021,"owners_count":24158757,"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","status":"online","status_checked_at":"2025-07-30T02:00:09.044Z","response_time":70,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"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":"2024-12-02T02:33:19.339Z","updated_at":"2025-07-30T13:10:10.822Z","avatar_url":"https://github.com/citiususc.png","language":"C","funding_links":[],"categories":[],"sub_categories":[],"readme":"# FlinkBWA\nFlinkBWA is a new tool that exploits the capabilities of a Big Data technology as Apache Flink to boost the performance of one of the most widely adopted sequence aligner, the Burrows-Wheeler Aligner (BWA).\n\nThe current version of FlinkBWA (v0.1, July 2017) supports the following BWA algorithms:\n\n* **BWA-MEM**\n* **BWA-backtrack**\n* **BWA-SW**\n\nAll of them work with single-reads and paired-end reads.\n\nIf you use **SparkBWA** or **FlinkBWA**, please cite this article:\n\nJosé M. Abuin, Juan C. Pichel, Tomás F. Pena and Jorge Amigo. [\"SparkBWA: Speeding Up the Alignment of High-Throughput DNA Sequencing Data\"][5]. PLoS ONE 11(5), pp. 1-21, 2016.\n\nA version for Hadoop is available [here](https://github.com/citiususc/BigBWA).\n\nA version for Spark is available [here](https://github.com/citiususc/SparkBWA).\n\n\n# Project structure\nThe project keeps a standard Maven structure. The source code is in the *src/main* folder. Inside it, we can find two subfolders:\n\n* **java** - Here is where the Java code is stored.\n* **native** - Here the BWA native code (C) and the glue logic for JNI is stored.\n\n# Getting started\n\n## Requirements\nRequirements to build **FlinkBWA** are the same than the ones to [build BWA](https://github.com/lh3/bwa/blob/master/README.md), with the only exception that the *JAVA_HOME* environment variable should be defined. If not, you can define it in the */src/main/native/Makefile.common* file. \n\nIt is also needed to include the flag *-fPIC* in the *Makefile* of the considered BWA version. To do this, the user just need to add this option to the end of the *CFLAGS* variable in the BWA Makefile. Considering bwa-0.7.15, the original Makefile contains:\n\n\tCFLAGS=\t\t-g -Wall -Wno-unused-function -O2\n\nand after the change it should be:\n\n\tCFLAGS=\t\t-g -Wall -Wno-unused-function -O2 -fPIC\n\nAdditionaly, [Maven 3](https://maven.apache.org/install.html) is also required.\n\n## Building\nThe default way to build **FlinkBWA** is:\n\n\thttps://github.com/citiususc/FlinkBWA.git\n\tcd FlinkBWA\n\tmvn package\n\nThis will create the *target* folder, which will contain the *jar* file needed to run **FlinkBWA**:\n\n* **flink-bwa-0.1.jar** - jar file to launch with Flink.\n\n## Install Apache Flink\n\n### Prerequisites\n* To be able to run Flink, the only requirement is to have a working Java 7.x (or higher) installation.\n    * You can check your current java version using the command: **java -version**\n\n### Setup\nAn Apache Hadoop installation is not required to use Flink. If you plan to run Flink in YARN or process data stored in HDFS then select the version matching your installed Hadoop version.\n\n1. Download the latest Apache Flink stable release from [here](https://flink.apache.org/downloads.html).\n2. Unpack the downloaded archive.\n3. Navigate to the unpacked directory and start Flink (local or cluster) using the scripts located in the bin directory.\n    * ./bin/start-local.sh -\u003e start a local Flink cluster\n4. Check the JobManager’s web frontend at [http://localhost:8081](http://localhost:8081) and make sure everything is up and running. The web frontend should report a single available TaskManager instance.\n5. To stop Flink when you finish yor work use the corresponding stop-*.sh script located in the bin directory.\n    * ./bin/stop-local.sh -\u003e stop a local Flink cluster\n\nYou can find a quick start guide [here](https://ci.apache.org/projects/flink/flink-docs-release-1.3/quickstart/setup_quickstart.html).\n\n## Running FlinkBWA\n\nTODO\n\n## Accuracy\n\nTODO\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcitiususc%2Fflinkbwa","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fcitiususc%2Fflinkbwa","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcitiususc%2Fflinkbwa/lists"}