{"id":32611484,"url":"https://github.com/ctlab/itmo-assembler","last_synced_at":"2025-10-30T13:59:17.254Z","repository":{"id":78880414,"uuid":"136324827","full_name":"ctlab/itmo-assembler","owner":"ctlab","description":"ITMO Genome Assembler","archived":false,"fork":false,"pushed_at":"2022-03-22T08:09:45.000Z","size":17759,"stargazers_count":3,"open_issues_count":0,"forks_count":1,"subscribers_count":7,"default_branch":"master","last_synced_at":"2024-05-19T00:08:56.665Z","etag":null,"topics":["bioinformatics","genome-assembly"],"latest_commit_sha":null,"homepage":"","language":"Java","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/ctlab.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}},"created_at":"2018-06-06T12:21:50.000Z","updated_at":"2022-03-21T17:02:23.000Z","dependencies_parsed_at":"2023-07-14T08:19:43.066Z","dependency_job_id":null,"html_url":"https://github.com/ctlab/itmo-assembler","commit_stats":null,"previous_names":[],"tags_count":2,"template":false,"template_full_name":null,"purl":"pkg:github/ctlab/itmo-assembler","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ctlab%2Fitmo-assembler","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ctlab%2Fitmo-assembler/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ctlab%2Fitmo-assembler/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ctlab%2Fitmo-assembler/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/ctlab","download_url":"https://codeload.github.com/ctlab/itmo-assembler/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ctlab%2Fitmo-assembler/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":281818072,"owners_count":26566859,"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","status":"online","status_checked_at":"2025-10-30T02:00:06.501Z","response_time":61,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"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","genome-assembly"],"created_at":"2025-10-30T13:58:17.773Z","updated_at":"2025-10-30T13:59:17.245Z","avatar_url":"https://github.com/ctlab.png","language":"Java","funding_links":[],"categories":[],"sub_categories":[],"readme":"**ITMO *de novo* Genome Assembler** is a software for assembling small and middle-sized genomes with ease. \u003cbr/\u003e\nIt had been developed by the team of researchers from Genome Assembly Algorithms Laboratory (now — bioinformatics group in [Computer Technologies Laboratory](http://ctlab.ifmo.ru/)) at ITMO University with the participation of the \"Bioengineering\" center of Russian Academy of Sciences. \n\nActive development of the software had been conducted from 2010 to 2016. \u003cbr/\u003e\nCurrently the main functionality of the assembler is supported, but without further improvements.\n\n\nSupported sequencing technologies - *Illumina*/*Solexa*, *Ion Torrent* (with indel errors) and *Sanger*.\u003cbr/\u003e\nAssembler can use both paired reads (paired-end, mate-pair) as well as unpaired ones.\u003cbr/\u003e\nThe assembly can be started both from command line as well as from simple and clear graphical user interface:\u003cbr/\u003e\n\n\u003cp align=\"center\"\u003e\n  \u003cimg src=\"GUI-paired.png\" height=\"350\" alt=\"GUI example\" /\u003e\n\u003c/p\u003e\n\n\n\n## Content\n\n* [First run](#first-run)\n* [Examples](#examples)\n* [Publications](#publications)\n* [Contact](#contact)\n\n\n## First run\n\nTo run the assembler *JRE* 1.6 or higher is required (you can download it \u003ca href=\"http://www.oracle.com/technetwork/java/javase/downloads/index.html\"\u003ehere\u003c/a\u003e).\u003cbr/\u003e\nNo other packages are required, you only need to download one running script.\n\n\nYou can download running script from the last stable release in the GitHub ['Releases' page](https://github.com/ctlab/itmo-assembler/releases).\u003cbr/\u003e\nDownload:\n* `itmo-assembler.sh` — for Unix-like OS (tested on Ubuntu, Debian and Mac OS). After downloading add a permission to run the script via command `chmod +x itmo-assembler.sh` and run it via `./itmo-assembler.sh`.\n* `itmo-assembler.bat` — for Windows OS (tested on Windows 7); \n* `itmo-assembler.jar` — for other platforms.\n\n\nAfter running this command the graphical user interface will arise.\u003cbr/\u003e\nIf you want to work with the assembler from the command line, add `-h` option to the command and the assembler will print the instructions how to start the assembly.\n\nBefore starting the assembly please make sure that there is enough free space on your hard drive. The assembler makes temporary files in working directory in order to be able to continue run from any stage.\n\n\n\n## Examples\n\n**Example 1.** Download file with unpaired reads [test1_unpaired.fastq](https://github.com/ctlab/itmo-assembler/raw/master/test_data/test1_unpaired.fastq) from `test_data` directory.\u003cbr/\u003e\nStart the assembly via command\n~~~\nitmo-assembler.sh -i test1_unpaired.fastq\n~~~\nor using graphical user interface:\u003cbr/\u003e\n\u003cp align=\"center\"\u003e\n  \u003cimg src=\"GUI-unpaired.png\" height=\"350\" alt=\"IMG\" /\u003e\n\u003c/p\u003e\n\n\nAfter the assembly will finish, assembled contigs' statistics will be printed:\u003cbr/\u003e\n```\nStatistics:\nTotal contigs: 1\nContigs\u003e=500bp: 1\nTotal length: 641'766\nMaximal length: 641'766\nMean length: 641'766\nMinimal length: 641'766\nN50: 641'766\nN90: 641'766\n```\nAssembled contigs will be placed in `workDir/contigs.fasta`. `workDir` directory is created in the directory, from which the assembler was started.\u003cbr/\u003e\u003cbr/\u003e\n\n\n**Example 2.** Download files with paired reads (left and right reads) — [test2_pair1.fastq](https://github.com/ctlab/itmo-assembler/raw/master/test_data/test2_pair1.fastq) and [test2_pair2.fastq](https://github.com/ctlab/itmo-assembler/raw/master/test_data/test2_pair2.fastq).\u003cbr/\u003e\nStart the assembly via command\n~~~\nitmo-assembler.sh -i test2_pair1.fastq test2_pair2.fastq\n~~~\nor using graphical user interface:\u003cbr/\u003e\n\u003cp align=\"center\"\u003e\n  \u003cimg src=\"GUI-paired.png\" height=\"350\" alt=\"IMG\" /\u003e\n\u003c/p\u003e\n\nAfter the assembly will finish, assembled contigs' statistics will be printed:\u003cbr/\u003e\n```\nStatistics:\nTotal contigs: 61\nContigs\u003e=500bp: 61\nTotal length: 649'946\nMaximal length: 49'875\nMean length: 10'655\nMinimal length: 529\nN50: 21'925\nN90: 8'213\n```\n\u003cbr/\u003e\n\n---\n\nThe assembler is freely distributed under the MIT License. \n\nPrevious versions of the assembler can be found at [genome.ifmo.ru/files/software/assembler](http://genome.ifmo.ru/files/software/assembler).\n\n### Publications:\n\n1. Alexandrov A., Kazakov S., Melnikov S., Sergushichev A., Shalyto A., Tsarev F. Combining de Bruijn graph, overlap graph and microassembly for de novo genome assembly / In Proceedings of \"Bioinformatics 2012\". Stockholm, Sweden. 2012. p. 72. [[Abstract pdf](http://rain.ifmo.ru/~svkazakov/papers/alexandrov-bioinf-2012-abstract.pdf)] [[Poster pdf](http://rain.ifmo.ru/~svkazakov/papers/alexandrov-bioinf-2012-poster.pdf)]\n2. **[In Russian]** Сергушичев А., Александров А., Казаков С., Царев Ф., Шалыто А. Совместное применение графа де Брёйна, графа перекрытий и микросборки для de novo сборки генома // Известия Саратовского университета. Новая серия. Серия Математика. Механика. Информатика. 2013. Т. 13, вып. 2, ч. 2, с. 51–57. [[pdf](http://rain.ifmo.ru/~svkazakov/papers/sergushichev-isu-2013.pdf)]\n3. **[In Russian]** Александров А., Казаков С., Мельников С., Сергушичев А., Царев Ф. Метод сборки контигов геномных последовательностей на основе совместного применения графов де Брюина и графов перекрытий // Научно-технический вестник информационных технологий, механики и оптики. 2012. № 6 (82), с. 93-98. [[pdf](http://rain.ifmo.ru/~svkazakov/papers/alexandrov-vestnik-itmo-2012.pdf)]\n4. **[In Russian]** Александров А., Казаков С., Мельников С., Сергушичев А., Царев Ф., Шалыто А. Метод исправления ошибок в наборе чтений нуклеотидной последовательности // Научно-технический вестник Санкт-Петербургского государственного университета информационных технологий, механики и оптики. 2011. № 5 (75), с. 81-84. [[pdf](http://rain.ifmo.ru/~svkazakov/papers/alexandrov-vestnik-itmo-2011-5.pdf)]\n\u003cbr/\u003e\u003cbr/\u003e\n\n\nSeveral tools are using the assembler as a library for better processing — such as [MetaFast](http://dx.doi.org/10.1093/bioinformatics/btw312) and [MetaCherchant](http://dx.doi.org/10.1093/bioinformatics/btx681).\n\n\n## Contact\n\nFor any questions please write us to genome@mail.ifmo.ru.\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fctlab%2Fitmo-assembler","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fctlab%2Fitmo-assembler","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fctlab%2Fitmo-assembler/lists"}