{"id":13743767,"url":"https://github.com/voutcn/megahit","last_synced_at":"2025-10-21T05:22:23.225Z","repository":{"id":21151386,"uuid":"24453792","full_name":"voutcn/megahit","owner":"voutcn","description":"Ultra-fast and memory-efficient (meta-)genome assembler","archived":false,"fork":false,"pushed_at":"2024-04-30T05:02:24.000Z","size":3200,"stargazers_count":644,"open_issues_count":103,"forks_count":136,"subscribers_count":37,"default_branch":"master","last_synced_at":"2025-03-03T23:51:27.548Z","etag":null,"topics":["bioinformatics","data-structures","genome-assembly","genomics","metagenomics","succinct"],"latest_commit_sha":null,"homepage":"http://www.ncbi.nlm.nih.gov/pubmed/25609793","language":"C++","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/voutcn.png","metadata":{"files":{"readme":"README.md","changelog":"CHANGELOG.md","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}},"created_at":"2014-09-25T10:29:18.000Z","updated_at":"2025-02-17T12:26:57.000Z","dependencies_parsed_at":"2023-02-14T19:55:42.829Z","dependency_job_id":"d4c3ad03-2d0b-4b87-aef9-34086ac0c32c","html_url":"https://github.com/voutcn/megahit","commit_stats":{"total_commits":610,"total_committers":16,"mean_commits":38.125,"dds":0.0721311475409836,"last_synced_commit":"5f329c6d24a1480b75145a4c14567a25453b95bf"},"previous_names":[],"tags_count":41,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/voutcn%2Fmegahit","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/voutcn%2Fmegahit/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/voutcn%2Fmegahit/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/voutcn%2Fmegahit/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/voutcn","download_url":"https://codeload.github.com/voutcn/megahit/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":253174364,"owners_count":21865852,"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","data-structures","genome-assembly","genomics","metagenomics","succinct"],"created_at":"2024-08-03T05:00:56.734Z","updated_at":"2025-10-21T05:22:23.218Z","avatar_url":"https://github.com/voutcn.png","language":"C++","funding_links":[],"categories":["C++","Assembly tools"],"sub_categories":["Metagenome \u0026 Metatranscriptome assembly"],"readme":"MEGAHIT\n=======\n\n[![BioConda Install](https://img.shields.io/conda/dn/bioconda/megahit.svg?style=flat-square\u0026label=BioConda%20install)](https://anaconda.org/bioconda/megahit)\n[![Downloads](https://img.shields.io/github/downloads/voutcn/megahit/total?style=flat-square)](https://github.com/voutcn/megahit/releases)\n[![Build Status](https://img.shields.io/travis/voutcn/megahit?style=flat-square)](https://travis-ci.org/voutcn/megahit)\n[![codecov](https://img.shields.io/codecov/c/github/voutcn/megahit?style=flat-square)](https://codecov.io/gh/voutcn/megahit)\n\nMEGAHIT is an ultra-fast and memory-efficient NGS assembler. It is optimized for metagenomes, but also works well on generic single genome assembly (small or mammalian size) and single-cell assembly.\n\nInstallation\n---------------\n\n### Conda\n```sh\nconda install -c bioconda megahit\n```\n\n### Guix\n```sh\nguix install megahit\n```\n\n### Pre-built binaries for x86_64 Linux\n\n```sh\nwget https://github.com/voutcn/megahit/releases/download/v1.2.9/MEGAHIT-1.2.9-Linux-x86_64-static.tar.gz\ntar zvxf MEGAHIT-1.2.9-Linux-x86_64-static.tar.gz\ncd MEGAHIT-1.2.9-Linux-x86_64-static/bin/\n./megahit --test  # run on a toy dataset\n./megahit -1 MY_PE_READ_1.fq.gz -2 MY_PE_READ_2.fq.gz -o MY_OUTPUT_DIR\n```\n\n### Pre-built docker image\n``` sh\n# in the directory with the input reads\ndocker run -v $(pwd):/workspace -w /workspace --user $(id -u):$(id -g) vout/megahit \\\n  -1 MY_PE_READ_1.fq.gz -2 MY_PE_READ_2.fq.gz -o MY_OUTPUT_DIR\n```\n\n### Building from source\n\n#### Prerequisites\n\n-   For building: zlib, cmake \u0026gt;= 2.8, g++ \u0026gt;= 4.8.4\n-   For running: gzip and bzip2\n\n```sh\ngit clone https://github.com/voutcn/megahit.git\ncd megahit\ngit submodule update --init\nmkdir build \u0026\u0026 cd build\ncmake .. -DCMAKE_BUILD_TYPE=Release  # add -DCMAKE_INSTALL_PREFIX=MY_PREFIX if needed\nmake -j4\nmake simple_test  # will test MEGAHIT with a toy dataset\n# make install if needed\n```\n\nUsage\n-----\n\n### Basic usage\n```sh\nmegahit -1 pe_1.fq -2 pe_2.fq -o out  # 1 paired-end library\nmegahit --12 interleaved.fq -o out # one paired \u0026 interleaved paired-end library\nmegahit -1 a1.fq,b1.fq,c1.fq -2 a2.fq,b2.fq,c2.fq -r se1.fq,se2.fq -o out # 3 paired-end libraries + 2 SE libraries\nmegahit_core contig2fastg 119 out/intermediate_contigs/k119.contig.fa \u003e k119.fastg # get FASTG from the intermediate contigs of k=119\n```\nThe contigs can be found `final.contigs.fa` in the output directory.\n\n### Advanced usage\n- `--kmin-1pass`: if sequencing depth is low and too much memory used when build the graph of k_min\n- `--presets meta-large`: if the metagenome is complex (i.e., bio-diversity is high, for example soil metagenomes)\n- `--cleaning-rounds 1 --disconnect-ratio 0`: get less pruned assembly (usually shorter contigs)\n- `--continue -o out`: resume an interrupted job from `out`\n\nTo see the full manual, run `megahit` without parameters or with `-h`.\n\nAlso, our [wiki](https://github.com/voutcn/megahit/wiki) may be helpful.\n\n### Examples\n\nThere is an example of a real assembly on this [wiki page](https://github.com/voutcn/megahit/wiki/An-example-of-real-assembly) \nand its corresponding [interactive Jupyter notebook](https://biotutorials.org/megahit). Contributed by Noah Lebovic (@lebovic).\n\nPublications\n------------\n\n-   Li, D., Liu, C-M., Luo, R., Sadakane, K., and Lam, T-W., (2015) MEGAHIT: An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. *Bioinformatics*, doi: 10.1093/bioinformatics/btv033 \\[PMID: [25609793](http://www.ncbi.nlm.nih.gov/pubmed/25609793)\\].\n-   Li, D., Luo, R., Liu, C.M., Leung, C.M., Ting, H.F., Sadakane, K., Yamashita, H. and Lam, T.W., 2016. MEGAHIT v1.0: A Fast and Scalable Metagenome Assembler driven by Advanced Methodologies and Community Practices. Methods.\n\nLicense\n-------\n\nThis project is licensed under the GPLv3 License - see the [LICENSE](LICENSE) file for details\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fvoutcn%2Fmegahit","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fvoutcn%2Fmegahit","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fvoutcn%2Fmegahit/lists"}