{"id":49195554,"url":"https://github.com/jackburton-qub/grace","last_synced_at":"2026-04-23T10:01:39.180Z","repository":{"id":351817637,"uuid":"1187345083","full_name":"jackburton-qub/GRACE","owner":"jackburton-qub","description":"Genomic Repeat Analysis and Characterisation Engine","archived":false,"fork":false,"pushed_at":"2026-04-16T15:50:41.000Z","size":1564,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":0,"default_branch":"master","last_synced_at":"2026-04-16T17:21:34.999Z","etag":null,"topics":["bioinformatics","blast","blastn","microsatellite","primer-design","pyqt6","ssr"],"latest_commit_sha":null,"homepage":"","language":"Python","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/jackburton-qub.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":"CITATION.cff","codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2026-03-20T16:09:06.000Z","updated_at":"2026-04-16T15:50:32.000Z","dependencies_parsed_at":null,"dependency_job_id":null,"html_url":"https://github.com/jackburton-qub/GRACE","commit_stats":null,"previous_names":["jackburton-qub/grace"],"tags_count":13,"template":false,"template_full_name":null,"purl":"pkg:github/jackburton-qub/GRACE","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/jackburton-qub%2FGRACE","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/jackburton-qub%2FGRACE/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/jackburton-qub%2FGRACE/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/jackburton-qub%2FGRACE/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/jackburton-qub","download_url":"https://codeload.github.com/jackburton-qub/GRACE/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/jackburton-qub%2FGRACE/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":32175040,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-04-23T02:19:40.750Z","status":"ssl_error","status_checked_at":"2026-04-23T02:17:55.737Z","response_time":53,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.5:443 state=error: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"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":["bioinformatics","blast","blastn","microsatellite","primer-design","pyqt6","ssr"],"created_at":"2026-04-23T10:01:38.490Z","updated_at":"2026-04-23T10:01:39.175Z","avatar_url":"https://github.com/jackburton-qub.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# GRACE\n### Genomic Repeat Analysis and Characterisation Engine\n\nGRACE is a standalone, offline, cross‑platform desktop application for microsatellite (SSR) marker development. It combines SSR detection, Primer3‑based primer design, BLAST specificity filtering, genomic annotation, and lab‑ready exports in a single graphical interface — no command line needed.\n\n---\n\n## Features\n\n- **SSR Detection** – fast regex‑based scanning for di‑ to hexanucleotide repeats, with canonical motif standardisation and optional adjacent‑motif filtering.\n- **SSR Summary** – interactive karyotype view showing SSR positions along chromosomes, motif type distribution, and genomic feature breakdown (exon/intron/intergenic) when a GFF is loaded.\n- **Primer Design** – Primer3‑powered design with quality filters. Two parameter presets:\n  - **Capillary Electrophoresis** – optimised for fragment analysis (M13 tails, dye multiplexing).\n  - **Amplicon Sequencing** – optimised for Illumina amplicon panels (P5/P7 tails, tight Tm, short products).\n- **Specificity Checking** – bundled BLAST+ binaries; no external installation required.\n- **GFF Annotation** – optional GFF3/GTF support for exon/intron/intergenic classification and chromosome name mapping.\n- **Three Complete Workflows**\n  - **Amplicon Sequencing** – validate multiplex primer pools for dimer risks, amplicon size, and GC content. Optimise panels and export tailed primers with amplicon reference sequences.\n  - **Capillary Electrophoresis** – assign dyes (FAM, VIC, NED, PET) and size bins. Supports multiple panels (injections) and exports ready‑to‑order primers with M13 tails.\n  - **GBS‑RE (Restriction‑Enzyme GBS)** – discover SSRs located within user‑defined restriction fragments (e.g. PstI‑MspI). Compare enzyme combinations, generate barcodes, and export marker lists.\n- **Linkage Disequilibrium Filter** – thin markers by physical distance across all workflows.\n- **Chromosome View** – visualise marker positions on chromosomes or contigs throughout the application.\n- **Project Summary** – dynamic, tabbed summary of all completed steps with embedded charts. Export a comprehensive PDF report.\n\n---\n\n## Installation\n\n### Pre‑built Binaries\nDownload the latest release for your platform from the [Releases](https://github.com/jackburton-qub/GRACE/releases) page. Extract the folder and run `GRACE.exe` (Windows) or open `GRACE.app` (macOS). BLAST+ is bundled – no separate installation required.\n\n### Running from Source\n```bash\ngit clone https://github.com/jackburton-qub/GRACE.git\ncd GRACE\npip install -r requirements.txt\npython main.py\nWorkflow\ntext\n01  Load Genome        – FASTA/FASTQ + optional GFF3/GTF annotation\n02  Detect SSRs        – scan for perfect repeats, annotate with genomic features\n03  SSR Summary        – visualise distribution and statistics\n04  Design Primers     – Capillary or Amplicon Sequencing mode\n05  Check Specificity  – BLAST primers against the genome\n06  BLAST Results      – review and filter by specificity\n07  Project Summary    – complete pipeline overview with PDF export\n08  Amplicon Tools     – multiplex validation and panel optimisation\n09  Capillary Tools    – dye assignment and size binning\n10  GBS‑RE Tools       – restriction fragment marker discovery\nDependencies\nPackage\tPurpose\nPyQt6\tDesktop GUI framework\nprimer3‑py\tPrimer design\npandas\tData handling\nnumpy\tNumerical operations\nreportlab\tPDF report generation\nBLAST+\tBundled – specificity checking\nSupported File Formats\nFormat\tInput\tOutput\nFASTA (.fa, .fasta, .fna)\t✓\t\nFASTQ (.fastq, .fq)\t✓\t\nGenBank (.gb, .gbff, .gbk)\t✓\t\nGFF3 (.gff, .gff3)\t✓\t\nGTF (.gtf)\t✓\t\nCSV\t\t✓\nFASTA (primers, amplicons)\t\t✓\nPDF\t\t✓\nJSON (session)\t✓\t✓\nLicence\nMIT – see LICENSE for details.","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fjackburton-qub%2Fgrace","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fjackburton-qub%2Fgrace","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fjackburton-qub%2Fgrace/lists"}