{"id":25983656,"url":"https://github.com/leonardogemin/duohash","last_synced_at":"2026-03-10T05:04:19.056Z","repository":{"id":245128063,"uuid":"817342516","full_name":"leonardoGemin/DuoHash","owner":"leonardoGemin","description":"DuoHash is an advanced tool for the efficient calculation of forward and reverse hashes of spaced k-mers in nucleotide sequences, improving the analysis of genomic data by reducing processing time and computational resources.","archived":false,"fork":false,"pushed_at":"2024-08-06T06:42:57.000Z","size":719,"stargazers_count":0,"open_issues_count":0,"forks_count":1,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-12-09T18:51:04.966Z","etag":null,"topics":["algorithm-optimization","bioinformatics","computational-biology","dna-sequencing","genomics","hashing","sequence-analysis","spaced-kmer"],"latest_commit_sha":null,"homepage":"","language":"Roff","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/leonardoGemin.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":"2024-06-19T13:59:29.000Z","updated_at":"2024-08-06T06:43:01.000Z","dependencies_parsed_at":"2024-06-20T00:51:56.310Z","dependency_job_id":"321dafcb-894b-4942-a2bd-2fc20e91a53a","html_url":"https://github.com/leonardoGemin/DuoHash","commit_stats":null,"previous_names":["leonardogemin/duohash"],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/leonardoGemin/DuoHash","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/leonardoGemin%2FDuoHash","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/leonardoGemin%2FDuoHash/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/leonardoGemin%2FDuoHash/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/leonardoGemin%2FDuoHash/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/leonardoGemin","download_url":"https://codeload.github.com/leonardoGemin/DuoHash/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/leonardoGemin%2FDuoHash/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":30325603,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-03-10T01:36:58.598Z","status":"online","status_checked_at":"2026-03-10T02:00:06.579Z","response_time":106,"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":["algorithm-optimization","bioinformatics","computational-biology","dna-sequencing","genomics","hashing","sequence-analysis","spaced-kmer"],"created_at":"2025-03-05T10:31:39.893Z","updated_at":"2026-03-10T05:04:19.032Z","avatar_url":"https://github.com/leonardoGemin.png","language":"Roff","funding_links":[],"categories":[],"sub_categories":[],"readme":"# DuoHash: Improving Spaced k-mer Extraction and Hash Encoding for Bioinformatics Applications\n\n\n## Methods\nThe **DuoHash** library provides two classes: **DuoHash** and **DuoHash_multi** for handling one or multiple spaced seeds, respectively. The methods of the first class are\n- `GetEncoding_naive()`,\n- `GetEncoding_FSH()`,\n- and `GetEncoding_ISSH()`.\n\nThe methods of the second class are\n- `GetEncoding_naive()`,\n- `GetEncoding_FSH()`,\n- `GetEncoding_ISSH()`,\n- `GetEncoding_FSH_multi()`,\n- `GetEncoding_MISSH_v1()`,\n- `GetEncoding_MISSH_col()`,\n- `GetEncoding_MISSH_col_parallel()`,\n- and `GetEncoding_MISSH_row()`.\n\nBoth classes share the `PrintFASTA()` method for saving the resulting spaced k-mers to a file and other methods for handling the various parameters.\n\nEach `GetEncoding_\u003c...\u003e()` method has four implementations. The first is for the extraction of spaced k-mer and their encoding only, the second allows post-processing of encodings to calculate forward and reverse hashing, the third allows post-processing of encodings for conversion into strings, and the fourth combines the two previous options.\n\n\n## Installation\nMake sure CMake is installed on the system.\n\nDownload the repository using\n```shell\n$ git clone https://github.com/leonardoGemin/DuoHash.git\n```\nand build the library with \n```shell\n$ make build\n```\n\nThis will install `build/libDuoHash.a` in the project's directory.\n\n\n## Usage\nTo use **DuoHash** in a C++ project:\n- Import DuoHash in the code using `#include \u003cDuoHash.h\u003e`\n- Add the `include` directory (pass `-I./include` to the compiler)\n- Link the code with `libDuoHash.a` (pass `-L./build -lDuoHash` to the compiler)\n- Compile your code with `g++-13`, `-std=c++0x` (and preferably `-O3`), and `-fopenmp` enabled\n\n\n## Example\nCompile `example/main.cpp` file with\n```shell\n$ cd example\n$ g++-13 -std=c++0x -O3 -fopenmp -I../include -L../build -lDuoHash -o main main.cpp\n```\n\n\n## Thesis\nLink to my Master Thesis: [Gemin_Leonardo.pdf](https://thesis.unipd.it/retrieve/99e7ee7c-1348-45f6-8a02-467bae6b0dbc/Gemin_Leonardo.pdf)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fleonardogemin%2Fduohash","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fleonardogemin%2Fduohash","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fleonardogemin%2Fduohash/lists"}