{"id":27317072,"url":"https://github.com/pdimens/mimick","last_synced_at":"2026-06-08T23:01:52.250Z","repository":{"id":286893708,"uuid":"962829632","full_name":"pdimens/mimick","owner":"pdimens","description":"Linked-read sequence simulator","archived":false,"fork":false,"pushed_at":"2025-06-20T17:56:04.000Z","size":14096,"stargazers_count":1,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-06-21T10:07:08.921Z","etag":null,"topics":["fastq","genomics","genomics-data","genomics-simulations","linked-reads"],"latest_commit_sha":null,"homepage":"https://pdimens.github.io/mimick/","language":"Python","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/pdimens.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,"zenodo":null}},"created_at":"2025-04-08T18:28:50.000Z","updated_at":"2025-06-20T17:56:07.000Z","dependencies_parsed_at":"2025-05-23T17:44:39.942Z","dependency_job_id":"189ee004-14d7-4f38-a165-4b29a1a0ddc0","html_url":"https://github.com/pdimens/mimick","commit_stats":null,"previous_names":["pdimens/mimick"],"tags_count":13,"template":false,"template_full_name":null,"purl":"pkg:github/pdimens/mimick","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pdimens%2Fmimick","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pdimens%2Fmimick/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pdimens%2Fmimick/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pdimens%2Fmimick/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/pdimens","download_url":"https://codeload.github.com/pdimens/mimick/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pdimens%2Fmimick/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":261103452,"owners_count":23109932,"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":["fastq","genomics","genomics-data","genomics-simulations","linked-reads"],"created_at":"2025-04-12T08:40:09.698Z","updated_at":"2026-06-08T23:01:52.244Z","avatar_url":"https://github.com/pdimens.png","language":"Python","funding_links":[],"categories":["Contributions"],"sub_categories":["Constellation"],"readme":"# Mimick\nLinked-read sequence simulator\n\n![mimick_logo](/docs/static/mimick_logo.png)\n\n[![gitHub release](https://img.shields.io/github/v/release/pdimens/mimick?style=for-the-badge\u0026logo=anaconda\u0026logoColor=ffffff)](https://github.com/pdimens/mimick/releases)\n[![documentation badge](https://img.shields.io/badge/read%20the-docs-daa355?style=for-the-badge\u0026logo=quicklook\u0026logoColor=ffffff)](https://pdimens.github.io/mimick)\n[![harpy badge](https://custom-icon-badges.demolab.com/badge/-Harpy-79a9b9?style=for-the-badge\u0026logo=package\u0026logoColor=ffffff)](https://www.github.com/pdimens/harpy)\n[![visor badge](https://custom-icon-badges.demolab.com/badge/-VISOR-12922e?style=for-the-badge\u0026logo=package\u0026logoColor=ffffff)](https://github.com/davidebolo1993/VISOR)\n\nOriginally known as XENIA from the [VISOR](https://github.com/davidebolo1993/VISOR) project, Mimick is a \nsimulator for linked-read FASTQ data. It allows you to simulate an\narbitrary number of haplotypes, set overall coverage, molecule coverage,\nand choose what kind of linked reads you want.\n\n## Supported Linked-Read Types\n- 10X\n- Haplotagging\n- stLFR\n- TELLseq\n\n## Simulation parameters\n- output FASTQ format\n- overall coverage depth\n- average molecule length\n- molecule coverage / reads per molecule\n- molecules per barcode (barcode convolution)\n- proportion of singletons (unlinked barcodes)\n- standard Illumina read characteristics e.g. read length, insert size, etc.\n\n## Standout Features\nOther than the fun name and logo, Mimick is an improvement over existing linked-read simulators in multiple ways:\n\n1. It's the only simulator (we are aware of) that isn't configured for discontinued-in-2019 10X linked-read chemistry and is instead \ngeneralized for existing options, both in terms of data formats and the simulation process itself.\n2. Circular DNA support. Yay prokaryotes!\n3. Mimick provides more parameters to tune your simulations for realistic linked-read library simulation in the form of singletons and \nmolecule coverage. These characteristics are **very** important regarding the performance of a linked-read library.\n4. Mimick uses a barcode-first simulation approach (v2+), which allows barcodes to be shared **across**\nchromosomes/contigs **and** haplotypes. This form of barcode sharing is a common phenomenon in real linked-read\nlibraries, but a characteristic existing simulators don't capture (e.g. XENIA only allowed barcode sharing within\na chromosome within a haplotype). The documentation explains this in better detail.\n6. `N` bases in the FASTA haplotypes can be replaced with random ATCG bases on the fly\n6. It supports multi-sample simulation (v3+) by way of one FASTA and one VCF as input. Sample haplotypes\nare made by applying SNP and indel variants from VCF to the contigs in the FASTA.\n7. It's fast. The Julia version (v3+) is a signficant speedup for single-sample simulation and the multi-sample simulation\nis parallelized across samples.\n\n### Authors\n#### Mimick\n\u003cimg src=\"https://avatars.githubusercontent.com/u/19176506?v=4\" width=\"50\" height=\"50\" style=\"border-radius: 50%; object-fit: cover;\"/\u003e [@pdimens](https://github.com/pdimens)\n\n#### VISOR\n\u003cimg src=\"https://avatars.githubusercontent.com/u/39052119?v=4\" width=\"50\" height=\"50\" style=\"border-radius: 50%; object-fit: cover;\"/\u003e [@davidebolo1993](https://github.com/davidebolo1993)\n\n\u003e [!NOTE]\n\u003e Why name it \"mimick\"? Well, this software mimics linked-read data, I have an affinity for naming software after\n\u003e [fictional monsters](https://en.wikipedia.org/wiki/Mimic_(Dungeons_%26_Dragons)) and \"mimick\" (with a \"k\") is the old-English\n\u003e spelling of the word, leaving `mimic` available for some other bioinformatician to use for a less farcical reason. Despite the\n\u003e lore of mimics being deadly traps, this software is anything but, I promise.\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpdimens%2Fmimick","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fpdimens%2Fmimick","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpdimens%2Fmimick/lists"}