{"id":21251270,"url":"https://github.com/datngu/circall_quant","last_synced_at":"2026-01-02T15:13:58.083Z","repository":{"id":194292316,"uuid":"689994889","full_name":"datngu/circall_quant","owner":"datngu","description":"Circall_quant: fast circRNA quantification with Quasi-mapping","archived":false,"fork":false,"pushed_at":"2023-09-13T15:12:30.000Z","size":461,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-01-21T20:48:47.350Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Nextflow","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/datngu.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":"2023-09-11T10:31:07.000Z","updated_at":"2023-09-12T12:45:19.000Z","dependencies_parsed_at":null,"dependency_job_id":"faa3221d-581d-49e2-a607-707ca564d28c","html_url":"https://github.com/datngu/circall_quant","commit_stats":null,"previous_names":["datngu/circall_quant"],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/datngu%2Fcircall_quant","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/datngu%2Fcircall_quant/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/datngu%2Fcircall_quant/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/datngu%2Fcircall_quant/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/datngu","download_url":"https://codeload.github.com/datngu/circall_quant/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":243686916,"owners_count":20331229,"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":"2024-11-21T03:41:18.473Z","updated_at":"2026-01-02T15:13:58.021Z","avatar_url":"https://github.com/datngu.png","language":"Nextflow","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Circall_quant: fast circRNA quantification with Quasi-mapping\n\n\n## 1. Introduction\n\nThis a a portable quantification module of cscQTL used for fast circRNA quantification with known highly confident circRNA candidates.\n\n## 2. Installation\n  \n\n### 2.0 Hardware requirement\n\n \n\nThe pipeline requires at least a linux system with 32 CPUs and 32GB of RAM to run. You may customize the requiment in the main.nf but generally not recommended.\n\n \n\n### 2.1 Dependency\n\n  \n\nSince Circall_quant is implemted with Nextflow (DSL2), you would need Nextflow to run it. Further information to install Nextflow can be found on its home page:[https://www.nextflow.io/](https://www.nextflow.io/)\n\n  \n\nFor tool dependency, I have placed all dependencies in their corresponding container, so you would need to run with Docker or Singularity.\n\n\nThe default desgins of Circall_quant is running with either Docker using a single machine (**-profile standard**) or with sigularity using slurm HPC(**-profile cluster**), you may need to change the **nextflow.config** to adapt to the your system.\n\n  \n\nFurther customization, I recommend to consult Nextflow homepage: [https://www.nextflow.io/docs/latest/config.html](https://www.nextflow.io/docs/latest/config.html)\n  \n\n### 2.2 Clone the pipeline\n\n  \n\n```sh\n\n \ngit clone  https://github.com/datngu/circall_quant.git\n\n\n```\n\n## 3. Parameters\n\n  \n| Parameters          | Description                                                                                                         | Default setting                        |\n| :------------------ | :------------------------------------------------------------------------------------------------------------------ | :------------------------------------- |\n| genome              | genome in fasta format                                                                                              | $baseDir/data/ref/genome.fa            |\n| cdna                | transcripts (cDNA) in fasta format                                                                                  | $baseDir/data/ref/cdna.fa              |\n| annotation          | ensembl annotation in gtf format                                                                                    | $baseDir/data/ref/annotation.gtf       |\n| reads               | ribo minus RNA seq reads in fastq.gz format                                                                         | $baseDir/data/reads/\\*\\_{1,2}.fastq.gz |\n| circRNA             | circRNA candidate list                                                                                              | $baseDir/data/circRNA_list.txt         |\n| trace\\_dir          | directory for tracing output - all intermediate files in the analyses will be soft-linked here - used for debugging | $baseDir/trace\\_dir                    |\n| outdir              | directory of output                                                                                                 | $baseDir/results                       |\n\n\n## 4. Test example\n\n\n\u003c!-- If you run in a local computer with Docker:\n\n```sh\n\nnextflow run main.nf -resume --reads $reads --outdir \"TEST_WITH_LOCAL\" --genotype $genotype --consensus 3 --coloc true --circall true --ciri2 true --circexplorer2 true -with-report -profile standard\n\n\n```\n\nIf you run in a HCP server with Singularity and Slurm:\n\n```sh\n\nnextflow run main.nf -resume --reads $reads --outdir \"TEST_WITH_HPC\" --genotype $genotype --consensus 3 --coloc true --circall true --ciri2 true --circexplorer2 true -with-report -profile cluster\n\n\n``` --\u003e\n\n\n\n## 5. License\n  \nCircall_quant uses GNU General Public License GPL-3.\n\n\n## 6. Reference\n\nDat Thanh Nguyen. 2023. \"An integrative framework for circular RNA quantitative trait locus discovery with application in human T cells.\" bioRxiv 2023.03.22.533756; doi: https://doi.org/10.1101/2023.03.22.533756\n\nNguyen, D. T., Trac, Q. T., Nguyen, T. H., Nguyen, H. N., Ohad, N., Pawitan, Y., \u0026 Vu, T. N. (2021). Circall: fast and accurate methodology for discovery of circular RNAs from paired-end RNA-sequencing data. BMC bioinformatics, 22, 1-18.\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n ","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdatngu%2Fcircall_quant","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fdatngu%2Fcircall_quant","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdatngu%2Fcircall_quant/lists"}