{"id":22895757,"url":"https://github.com/pseudogene/lamp-virus","last_synced_at":"2025-08-12T02:32:23.090Z","repository":{"id":79848617,"uuid":"59816798","full_name":"pseudogene/lamp-virus","owner":"pseudogene","description":"Pipeline to develop one-step real-time RT-LAMP assays for specific detection of virus","archived":false,"fork":false,"pushed_at":"2019-03-27T08:45:48.000Z","size":34,"stargazers_count":4,"open_issues_count":0,"forks_count":1,"subscribers_count":2,"default_branch":"master","last_synced_at":"2024-07-30T19:59:37.372Z","etag":null,"topics":["bioinformatics","docker","lamp","primer","scientific","virus"],"latest_commit_sha":null,"homepage":null,"language":"Perl","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/pseudogene.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE.md","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null}},"created_at":"2016-05-27T08:03:11.000Z","updated_at":"2021-12-17T15:37:14.000Z","dependencies_parsed_at":null,"dependency_job_id":"82516f44-8903-45c2-a755-06d4131dc13b","html_url":"https://github.com/pseudogene/lamp-virus","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pseudogene%2Flamp-virus","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pseudogene%2Flamp-virus/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pseudogene%2Flamp-virus/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pseudogene%2Flamp-virus/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/pseudogene","download_url":"https://codeload.github.com/pseudogene/lamp-virus/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":229629256,"owners_count":18101263,"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":["bioinformatics","docker","lamp","primer","scientific","virus"],"created_at":"2024-12-13T23:31:53.144Z","updated_at":"2024-12-13T23:31:53.733Z","avatar_url":"https://github.com/pseudogene.png","language":"Perl","funding_links":[],"categories":[],"sub_categories":[],"readme":"# lamp-virus\n\n[![Build Status](https://travis-ci.org/pseudogene/lamp-virus.svg?branch=master)](https://travis-ci.org/pseudogene/lamp-virus)\n\nWe foster the openness, integrity, and reproducibility of scientific research.\n\nScripts and tools used to develop one-step real-time RT-LAMP assays.\n\n## Associated publications\n\n\u003e **Development of four one-step real-time RT-LAMP assays for specific detection of dengue virus serotypes**.\n\u003e Lopez-Jimena B, Bekaert M, Bakheit M, Frischmann S, Patel P, Sakuntabhai A, Lambrechts L, Fall C, Faye O, Sall A and Weidmann M.\n\u003e_PLOS Negl. Trop. Dis._. 12(7): e0180625\n\n[![DOI](https://img.shields.io/badge/DOI-10.1371%2Fjournal.pntd.0006381-blue.svg)](https://doi.org/10.1371/journal.pntd.0006381)\n\n\u003e **Development of a single-tube one-step RT-LAMP assay to detect the Chikungunya virus genome**.\n\u003e Lopez-Jimena B, Wehner S, Harold G, Bakheit M, Frischmann S, Bekaert M, Faye O, Sall A and Weidmman M.\n\u003e_PLOS Negl. Trop. Dis._. 12(7): e0180625\n\n[![DOI](https://img.shields.io/badge/DOI-10.1371%2Fjournal.pntd.0006448-blue.svg)](https://doi.org/10.1371/journal.pntd.0006448)\n\n## How to use this repository?\n\nThis repository host both the scripts and tools developed by this study. Feel free to adapt the scripts and tools, but remember to cite their authors!\n\nTo look at our scripts and raw results, **browse** through this repository. If you want to reproduce our results you will need to **clone** this repository, build the docker, and the run all the scripts. If you want to use our data for our own research, **fork** this repository and **cite** the authors.\n\n\n## Prepare a docker\n\nAll required files and tools run in a self-contained [docker](https://www.docker.com/) image.\n\n#### Clone the repository\n\n```\ngit clone https://github.com/pseudogene/lamp-virus.git\ncd lamp-virus\n```\n\n#### Create a docker\n\n```\ndocker build --rm=true --file=Dockerfile -t lamp-virus .\n```\n\n#### Start the docker\n\nTo import and export the results of your analysis you need to link a folder to the docker. It this example your data will be store in `results` (current filesystem) which will be seem as been `/virus` from within the docker by using `-v \u003cUSERFOLDER\u003e:/virus`.\n\n```\nmkdir ~/results\ndocker run -i -t --rm -v ~/results:/virus lamp-virus /bin/bash\n```\n\n#### Run a new analysis\n\n**1** - Collect NCBI genomes, automatically aligned them with [GramAlign v3.0](http://bioinfo.unl.edu/gramalign.php) and run [R/adegenet](http://adegenet.r-forge.r-project.org/) on the alignment to generate PCA and phylogeny.\n\n```\ncollect_genomevirus.pl -p zika -q \"txid64320[Organism:exp]\" -a 2004 -b 2016\n```\n\nwhere:\n\n`-p` is the filename prefix for all output file.\n\n`-q` is the NCBI entrez query string. (e.g. Zika virus: \"txid64320[Organism:exp]\")\n\n`-a` (after) is the lower limit for the year.\n\n`-b` (before) is the upper limit for the year.\n\n**2** - In `/virus` (from within the docker) or `results` (from outside) you now have all the results files including PCA, phylogeny and TSV file.\n\nEdit the TSV (Tabulation Separated Values) genotype/group numbers you manually identified. The second column been calculated groups (to be used with the standard parameter sets), the third column been the more granular subgrouping (to be used with the --alt parameter)\n\ne.g.:\n\n```\nsequence_1   1   1\nsequence_2   1   2\nsequence_3   2   3\n```\n\n**3** - Retrieve the subgroups/genotypes from the TSV file and run [LAVA-DNA](https://github.com/dylanstorey/lava-dna) on each genotype and each combination.\n\n```\nclass_sequences.pl -p zika -a zika.align.fa -g zika.groups.tsv -c \u003e zika.log\nor\nclass_sequences.pl -p zika -a zika.align.fa -g zika.groups.edited.tsv -c -l \u003e zika.loose.log\n```\n\nwhere:\n\n`-p` is the filename prefix for all output file.\n\n`-a` is the alignment generated by GramAlign (fasta-align format).\n\n`-g` is the list of subgroups/genotypes (TSV file).\n\n`-c` allows to test combination of genotypes and not only each genotypes.\n\n`-l` allows for the `loose` parameter set rather than `standard` by [LAVA-DNA](https://github.com/dylanstorey/lava-dna).\n\n\n**4** - Then evaluate the best minimal set of primer and map each primer set\n\n```\nmap_lamp.pl -svg -a zika.align.fa \\\n -p zika.1.primers \\\n -p zika.2_5.primers \\\n -p zika.4.primers \\\n \u003e zika.svg\n```\n\nwhere:\n\n`-svg` or `-png` will generate a SVG or PNG image.\n\n`-a` is the alignment generated by GramAlign (fasta-align format).\n\n`-p` are lists of primer sets generated by `class_sequences.pl`.\n\n## Parameters\n\n![Additional description of a LAMP signature](https://static-content.springer.com/image/art%3A10.1186%2F1471-2105-12-240/MediaObjects/12859_2010_Article_4632_Fig1_HTML.jpg)\n\nAdditional description of a LAMP signature. Each named pair refers to a sequence location corresponding to the primer regions of like-numbered primers. These pairs represent the location and orientation of the primers with respect to the target template during each extension in which they participate.\n\n#### Super strict (\"Stricter\")\nParameter | Default Target\n--- | ---\nOuter primer length | 18-22 bp\nMiddle primer length | 18-22 bp\nLoop primer length | 18-22 bp\nInner primer length | 18-22 bp\nOuter primer Tm | 58-62°C\nMiddle primer Tm | 58-62°C\nLoop primer Tm | 60-64°C\nInner primer Tm | 63-67°C\nMaximum signature length | 180 bp\nMinimum spacing from middle to inner primers | 40 bp\nMaximum consecutive repeated bases | 4\n\n\n#### Strict\nParameter | Default Target\n--- | ---\nOuter primer length | 15-25 bp\nMiddle primer length | 15-25 bp\nLoop primer length | 15-25 bp\nInner primer length | 15-25 bp\nOuter primer Tm | 53-67°C\nMiddle primer Tm | 53-67°C\nLoop primer Tm | 55-69°C\nInner primer Tm | 58-72°C\nMaximum signature length | 200 bp\nMinimum spacing from middle to inner primers | 20 bp\nMaximum consecutive repeated bases | 4\n\n\n#### Standard\nDefault values of the most commonly adjusted LAVA parameters ([Torres et al, 2011](http://dx.doi.org/10.1186/1471-2105-12-240))\n\nParameter | Default Target\n--- | ---\nOuter primer length | 18-23 bp\nMiddle primer length | 18-23 bp\nLoop primer length | 18-23 bp\nInner primer length | 20-26 bp\nOuter primer Tm | 59-61°C\nMiddle primer Tm | 59-61°C\nLoop primer Tm | 58-62°C\nInner primer Tm | 62-66°C\nMaximum signature length | 320 bp\nMinimum spacing from middle to inner primers | 25 bp\nMaximum consecutive repeated bases | 5\n\n\n#### Loose\nParameter | Default Target\n--- | ---\nOuter primer length | 17-24 bp\nMiddle primer length | 17-24 bp\nLoop primer length | 17-24 bp\nInner primer length | 18-28 bp\nOuter primer Tm | 58-62°C\nMiddle primer Tm | 58-62°C\nLoop primer Tm | 57-63°C\nInner primer Tm | 61-66°C\nMaximum signature length | 400 bp\nMinimum spacing from middle to inner primers | 20 bp\nMaximum consecutive repeated bases | 5\n\n#### Very Loose (\"Looser\")\n\nParameter | Default Target\n--- | ---\nOuter primer length | 16-25 bp\nMiddle primer length | 16-25 bp\nLoop primer length | 16-25 bp\nInner primer length | 16-29 bp\nOuter primer Tm | 57-63°C\nMiddle primer Tm | 57-63°C\nLoop primer Tm | 56-64°C\nInner primer Tm | 68-67°C\nMaximum signature length | 500 bp\nMinimum spacing from middle to inner primers | 18 bp\nMaximum consecutive repeated bases | 6\n\n\n## Scripts\n#### collect_genomevirus.pl\n\n```\nUsage: collect_genomevirus.pl --prefix \u003coutput prefix\u003e --query \u003cNCBI entrez query\u003e [..]\nDescription: Collect all complete genomes using the provided ENTREZ query and align them.\n\n--prefix \u003cfile prefix\u003e\n    Filename output prefix. [mandatory]\n--query \u003cquery string\u003e\n    NCBI entrez query. [mandatory]\n--after \u003cyear\u003e\n    minimum date to retrieve from (YYYY).\n--before \u003cyear\u003e\n    maximum date to retrieve from (YYYY).\n--norun\n    Disable the automatic run of R and the PCA and cluster analysis\n--verbose\n    Becomes very chatty.\n```\n\n#### class_sequences.pl\n\n```\nUsage: class_sequences.pl --prefix \u003coutput prefix\u003e --align \u003caligned genomes\u003e --groups \u003clist of groups\u003e [..]\nDescription: Generate RT-LAMP primer sets for each group of genomes provided.\n\n--prefix \u003cfile prefix\u003e\n    Filename output prefix. [mandatory]\n--groups \u003cpath\u003e\n    Path to a TSV file with the genome groups (e.g. output.group.tsv). [mandatory]\n        sequence_id\u003ctab\u003egrouping\u003ctab\u003ealt_grouping\n        sequence_1       1           1\n        sequence_2       1           2\n        sequence_3       2           3\n\n--align \u003caligned genome\u003e\n    Alignment generated by collect_genomevirus.pl. [mandatory]\n--realign\n    Force each group or group combination to be realign prior running LAVA.\n--combinatory\n    Force to test group combinations (recommended).\n--extra \u003clava parameter file\u003e\n    Provide LAVA XML parameter file.\n--strict\n    Force usage of strict LAMP parameters (see documentation).\n--strict --strict\n    Force usage of even stricter LAMP parameters (see documentation).\n--loose\n    Force usage of loose LAMP parameters (see documentation).\n--loose --loose\n    Force usage of even looser LAMP parameters (see documentation).\n--alt\n    Force usage alternative grouping column from the group file.\n--verbose\n    Becomes very chatty.\n```\n\n#### map_lamp.pl\n\n```\nUsage: map_lamp.pl --align \u003caligned genomes\u003e --primer \u003clist 1 of primer\u003e [--primer \u003clist 2 of primer\u003e ...] [--svg|--png]\nDescription: Generate a simple visualisation of the location of the RT-LAMP primer on the alignment.\n\n--align \u003caligned genome\u003e\n    Alignment generated by collect_genomevirus.pl. [mandatory]\n--primer \u003cprimer file\u003e\n    Path to the primer file generated by class_sequence.pl. Can be use multiple time for multiple file.\n--svg\n    Produce a vectorial figure (SVG format).\n--png\n    Provide a bitmap figure (PNG format).\n--verbose\n    Becomes very chatty.\n```\n\n## Issues\n\nIf you have any problems with or questions about the scripts, please contact us through a [GitHub issue](https://github.com/pseudogene/lamp-virus/issues).\nAny issue related to the scientific results themselves must be done directly with the authors.\n\n\n## Contributing\n\nYou are invited to contribute new features, fixes, or updates, large or small; we are always thrilled to receive pull requests, and do our best to process them as fast as we can.\n\n\n## License and distribution\n\nThis code is distributed under the [GNU GPL license v3](http://www.gnu.org/licenses/gpl-3.0.html). The documentation, raw data and work are licensed under a [Creative Commons Attribution-ShareAlike 4.0 International License](http://creativecommons.org/licenses/by-sa/4.0/).​\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpseudogene%2Flamp-virus","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fpseudogene%2Flamp-virus","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpseudogene%2Flamp-virus/lists"}