{"id":25938686,"url":"https://github.com/karel-brinda/dymas","last_synced_at":"2026-03-08T13:35:22.829Z","repository":{"id":24622269,"uuid":"28031260","full_name":"karel-brinda/dymas","owner":"karel-brinda","description":"Dynamic Mapping Simulator.","archived":false,"fork":false,"pushed_at":"2016-11-19T13:47:01.000Z","size":43496,"stargazers_count":2,"open_issues_count":7,"forks_count":0,"subscribers_count":2,"default_branch":"master","last_synced_at":"2023-02-26T11:56:13.971Z","etag":null,"topics":["bioinformatics","ngs","read-mapping","simulation"],"latest_commit_sha":null,"homepage":"http://arxiv.org/abs/1605.09070","language":"HTML","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/karel-brinda.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}},"created_at":"2014-12-15T10:13:17.000Z","updated_at":"2021-12-15T17:42:53.000Z","dependencies_parsed_at":"2022-08-06T03:00:42.329Z","dependency_job_id":null,"html_url":"https://github.com/karel-brinda/dymas","commit_stats":null,"previous_names":[],"tags_count":null,"template":null,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/karel-brinda%2Fdymas","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/karel-brinda%2Fdymas/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/karel-brinda%2Fdymas/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/karel-brinda%2Fdymas/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/karel-brinda","download_url":"https://codeload.github.com/karel-brinda/dymas/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":241780472,"owners_count":20019058,"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","ngs","read-mapping","simulation"],"created_at":"2025-03-04T03:37:54.274Z","updated_at":"2026-03-08T13:35:17.797Z","avatar_url":"https://github.com/karel-brinda.png","language":"HTML","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Dynamic Mapping Simulator\n\n## Introduction\n\nThis is repository contains Dynamic Mapping Simulator and supporting information for the paper\nK. Břinda, V. Boeva, G. Kucherov: *Dynamic read mapping and online consensus calling for better variant detection* ([arXiv:1605.09070](http://arxiv.org/abs/1605.09070)).\n\n\nDynamic mapping is mapping to a reference, which is continuously corrected according to alignments computed so far. *Dynamic Mapping Simulator* is a pipeline to simulate dynamic mapping using existing software to evaluate its benefits in comparison to standard *static mapping* and *iterative referencing*. For more details, see the paper.\n\n## Simulation algorithm\n\nScheme of the simulation pipeline:\n\n![](docs/simulation_pipeline.png)\n\nReads are taken in the following way:\n\n![](docs/reads.png)\n\nSM = static mapping, DM = dynamic mapping without remapping, DM-remap = dynamic mapping with remapping, IR = iterative referencing\n\n## Structure of this repository\n\n* [docs](docs) - supplementary materials (S1 and S2 files)\n* [dymas](docs) - Dynamic Mapping Simulator (Python package)\n* [experiments](docs) - all runs of all experiments\n* [reports](reports) - generated reports\n\n## Reports\n\n## Replication of results\n\n### Prerequisities\n\n**Experiments**\n\n* Python 3.3/3.4\n* [OCOCO](http://github.com/karel-brinda/ococo)\n* [RNFtools](http://github.com/karel-brinda/rnftools)\n\n**Additional software for reports**\n\n* GNU Parallel\n* LaTeX\n* Inkscape\n* Gnuplot 5\n\n#### Recommended way of installation using [Anaconda](https://www.continuum.io/downloads)\n\nEnvironment installation:\n\n```bash\n\tconda create -y --name dymas \\\n\t  -c bioconda \\\n\t\tpython==3.4 \\\n\t\tsnakemake samtools git cmake gnuplot ococo numpy biopython pysam==0.8.3\n```\n\nEnvironment activation:\n\n```bash\nsource activate dymas\n```\n\nInstallation of Python packages (in the activated environment)\n\n```bash\npip install -r requirements.txt\n```\n\n### Replication steps\n\n0. Install all required software and activate the corresponding Conda environment.\n\n  ```bash\n\tsource activate dymas\n  ```\n\n1. Remove computed data\n\n  ```bash\n  make clean\n  ```\n\n2. Download reference genomes\n\n  ```bash\n  make -C experiments/exp0*\n  ```\n\n3. Run experiments (this step will take several hours)\n\n  ```bash\n  make -C experiments -j 10\n  ```\n\n4. Generate reports\n\n  ```bash\n  make -C reports -j 10\n  ```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fkarel-brinda%2Fdymas","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fkarel-brinda%2Fdymas","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fkarel-brinda%2Fdymas/lists"}