{"id":13675838,"url":"https://github.com/pachterlab/kallisto","last_synced_at":"2025-05-14T18:05:22.461Z","repository":{"id":23206092,"uuid":"26562905","full_name":"pachterlab/kallisto","owner":"pachterlab","description":"Near-optimal RNA-Seq quantification","archived":false,"fork":false,"pushed_at":"2025-04-09T09:57:14.000Z","size":9624,"stargazers_count":673,"open_issues_count":195,"forks_count":173,"subscribers_count":47,"default_branch":"master","last_synced_at":"2025-04-13T13:16:52.119Z","etag":null,"topics":["kallisto","pseudoalignment","rna-seq"],"latest_commit_sha":null,"homepage":"https://pachterlab.github.io/kallisto","language":"C","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":"indyplanets/flexnav","license":"bsd-2-clause","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/pachterlab.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"license.txt","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":"2014-11-13T00:27:48.000Z","updated_at":"2025-02-22T10:05:03.000Z","dependencies_parsed_at":"2023-10-15T07:50:48.035Z","dependency_job_id":"8b930630-a449-4d37-9205-32d5c26ca5d9","html_url":"https://github.com/pachterlab/kallisto","commit_stats":{"total_commits":1085,"total_committers":16,"mean_commits":67.8125,"dds":0.6672811059907834,"last_synced_commit":"ff32921dbeb4f9853984a88c1c7534562e256d7a"},"previous_names":[],"tags_count":21,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pachterlab%2Fkallisto","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pachterlab%2Fkallisto/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pachterlab%2Fkallisto/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pachterlab%2Fkallisto/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/pachterlab","download_url":"https://codeload.github.com/pachterlab/kallisto/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":254198514,"owners_count":22030965,"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":["kallisto","pseudoalignment","rna-seq"],"created_at":"2024-08-02T12:01:04.885Z","updated_at":"2025-05-14T18:05:17.450Z","avatar_url":"https://github.com/pachterlab.png","language":"C","funding_links":[],"categories":["Software packages"],"sub_categories":["RNA-seq"],"readme":"# kallisto\n\n__kallisto__ is a program for quantifying abundances of transcripts from\nRNA-Seq data, or more generally of target sequences using high-throughput\nsequencing reads. It is based on the novel idea of _pseudoalignment_ for\nrapidly determining the compatibility of reads with targets, without the need\nfor alignment. On benchmarks with standard RNA-Seq data, __kallisto__ can\nquantify 30 million human bulk RNA-seq reads in less than 3  minutes on a Mac desktop\ncomputer using only the read sequences and a transcriptome index that\nitself takes than 10 minutes to build. Pseudoalignment of reads\npreserves the key information needed for quantification, and __kallisto__\nis therefore not only fast, but also comparably accurate to other existing\nquantification tools. In fact, because the pseudoalignment procedure is\nrobust to errors in the reads, in many benchmarks __kallisto__\nsignificantly outperforms existing tools. The __kallisto__ algorithms are described in more detail in:\n\nNL Bray, H Pimentel, P Melsted and L Pachter, [Near optimal probabilistic RNA-seq quantification](http://www.nature.com/nbt/journal/v34/n5/abs/nbt.3519.html), Nature Biotechnology __34__, p 525--527 (2016).\n\nScripts reproducing all the results of the paper are available [here](https://github.com/pachterlab/kallisto_paper_analysis).\n\n__kallisto__ quantified bulk RNA-Seq can be analyzed with [__sleuth__](https://github.com/pachterlab/sleuth/).\n\n__kallisto__ can be used together with [__bustools__](https://bustools.github.io/) to pre-process single-cell RNA-seq data. See the [kallistobus.tools](https://www.kallistobus.tools/) website for instructions.\n\n## Manual\n\nPlease visit http://pachterlab.github.io/kallisto/manual.html for the manual.\n\n## License\n\n__kallisto__ is distributed under the BSD-2 license. The license is distributed with __kallisto__ in the file `license.txt`, which is also viewable [here](https://pachterlab.github.io/kallisto/download). Please read the license before using __kallisto__.\n\n## Getting help\n\nFor help running __kallisto__, please post to the [kallisto-and-applications Google Group](https://groups.google.com/forum/#!forum/kallisto-and-applications).\n\n## Reporting bugs\n\nPlease report bugs to the [Github issues page](https://github.com/pachterlab/kallisto/issues)\n\n## Development and pull requests\n\nWe typically develop on separate branches, then merge into devel once features\nhave been sufficiently tested. `devel` is the latest, stable, development\nbranch. `master` is used only for official releases and is considered to be\nstable. If you submit a pull request (thanks!) please make sure to request to\nmerge into `devel` and NOT `master`. Merges usually only go into `master`, but\nnot out.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpachterlab%2Fkallisto","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fpachterlab%2Fkallisto","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpachterlab%2Fkallisto/lists"}