# kallisto

> software for RNA-seq read quantification

**Wikidata**: [Q113047600](https://www.wikidata.org/wiki/Q113047600)  
**Source**: https://4ort.xyz/entity/kallisto

## Summary
kallisto is a software program designed for RNA-seq read quantification and transcript quantification. It is an open-source tool licensed under the 2-clause BSD License. The project is funded by the Chan Zuckerberg Initiative and its source code is maintained on GitHub by the Pachter Lab.

## Key Facts
- **Primary Use:** RNA-seq read quantification and transcript quantification.
- **License:** 2-clause BSD License.
- **Programming Languages:** C and C++.
- **Source Repository:** [https://github.com/pachterlab/kallisto](https://github.com/pachterlab/kallisto)
- **Website:** [https://pachterlab.github.io/kallisto/](https://pachterlab.github.io/kallisto/)
- **Funding:** Supported by the Chan Zuckerberg Initiative under the "Essential Open Source Software for Science program grant."
- **Initial Release:** Version 0.42 was released on May 6, 2015.
- **Latest Recorded Version:** Version 0.44.0 (released January 29, 2018).

## FAQs
### Q: What is the primary function of kallisto?
A: Kallisto is a software tool used for quantifying RNA-seq reads and transcripts. It processes sequencing data to determine the abundance of transcripts.

### Q: Under what license is kallisto distributed?
A: The software is distributed under the 2-clause BSD License, which allows for broad usage and modification with minimal restrictions.

### Q: Who funds the development of kallisto?
A: Development is funded by the Chan Zuckerberg Initiative specifically through their Essential Open Source Software for Science program grant.

## Why It Matters
Kallisto serves as a critical component in the bioinformatics workflow for RNA sequencing analysis. By providing a specific tool for transcript quantification, it enables researchers to process non-tangible executable data components generated by high-throughput sequencing machines. Its classification as "Essential Open Source Software for Science" by the Chan Zuckerberg Initiative underscores its importance in the scientific community, particularly for reproducibility and open access to data processing tools.

The software's development timeline, spanning from 2015 to 2018 in the provided records, shows active maintenance and versioning to support the evolving needs of genomic research. Its implementation in C and C++ suggests a focus on performance efficiency typical of computational biology tools handling large datasets.

## Notable For
- **Funding Recognition:** Recognized as "Essential Open Source Software for Science" by the Chan Zuckerberg Initiative.
- **Rapid Development Cycle:** Released ten distinct versions between May 2015 and January 2018.
- **Open Source Accessibility:** Freely available via GitHub under a permissive BSD license.
- **Technical Implementation:** Built using C and C++, languages often chosen for high-performance computational tasks.

## Body
### Software Classification and Use
Kallisto is classified as a non-tangible executable component of a computer (software) specifically designed for biological data analysis. Its primary use case is **transcript quantification** from RNA-seq data. The official Wikidata description defines it simply as "software for RNA-seq read quantification."

### Technical Specifications
The software is written in the **C** and **C++** programming languages. It is accessible to users via its official website hosted by Pachter Lab and its source code is publicly available on GitHub.
- **Source Code URL:** `https://github.com/pachterlab/kallisto`
- **Repository Identifiers:** GitHub (`Q186055`), Kallisto (`Q364` within the context of the repository ID P10627).

### Version History
The software has undergone multiple updates since its inception. The following versions are documented in the source material:
- **v0.42:** Released May 6, 2015.
- **v0.42.1:** Released May 13, 2015.
- **v0.42.2:** Released June 13, 2015.
- **v0.42.2.1:** Released June 19, 2015.
- **v0.42.3:** Released August 25, 2015.
- **v0.42.4:** Released October 29, 2015.
- **v0.42.5:** Released April 5, 2016.
- **v0.43.0:** Released June 3, 2016.
- **v0.43.1:** Released August 3, 2017.
- **v0.44.0:** Released January 29, 2018.

### Funding and Support
The development and maintenance of kallisto have been supported by the **Chan Zuckerberg Initiative**. This funding was provided specifically through the "Essential Open Source Software for Science program grant," as verified on September 6, 2022. The software operates under the **2-clause BSD License**, ensuring it remains free and open for scientific and commercial use.

## References

1. [Source](https://api.github.com/repos/pachterlab/kallisto)
2. [Release 0.42. 2015](https://github.com/pachterlab/kallisto/releases/tag/v0.42)
3. [Release 0.42.1. 2015](https://github.com/pachterlab/kallisto/releases/tag/v0.42.1)
4. [Release 0.42.2. 2015](https://github.com/pachterlab/kallisto/releases/tag/v0.42.2)
5. [Release 0.42.2.1. 2015](https://github.com/pachterlab/kallisto/releases/tag/v0.42.2.1)
6. [Release 0.42.3. 2015](https://github.com/pachterlab/kallisto/releases/tag/v0.42.3)
7. [Release 0.42.4. 2015](https://github.com/pachterlab/kallisto/releases/tag/v0.42.4)
8. [Release 0.42.5. 2016](https://github.com/pachterlab/kallisto/releases/tag/v0.42.5)
9. [Release 0.43.0. 2016](https://github.com/pachterlab/kallisto/releases/tag/v0.43.0)
10. [Release 0.43.1. 2017](https://github.com/pachterlab/kallisto/releases/tag/v0.43.1)
11. [Release 0.44.0. 2018](https://github.com/pachterlab/kallisto/releases/tag/v0.44.0)
12. [Release 0.45.0. 2018](https://github.com/pachterlab/kallisto/releases/tag/v0.45.0)
13. [Release 0.45.1. 2019](https://github.com/pachterlab/kallisto/releases/tag/v0.45.1)
14. [Release 0.46.0. 2019](https://github.com/pachterlab/kallisto/releases/tag/v0.46.0)
15. [Release 0.46.1. 2019](https://github.com/pachterlab/kallisto/releases/tag/v0.46.1)
16. [Release 0.46.2. 2020](https://github.com/pachterlab/kallisto/releases/tag/v0.46.2)
17. [Release 0.48.0. 2022](https://github.com/pachterlab/kallisto/releases/tag/v0.48.0)
18. [Release 0.50.0. 2023](https://github.com/pachterlab/kallisto/releases/tag/v0.50.0)
19. [Release 0.50.1. 2023](https://github.com/pachterlab/kallisto/releases/tag/v0.50.1)
20. [Release 0.51.0. 2024](https://github.com/pachterlab/kallisto/releases/tag/V0.51.0)
21. [Release 0.51.1. 2024](https://github.com/pachterlab/kallisto/releases/tag/v0.51.1)
22. [Release 0.52.0. 2026](https://github.com/pachterlab/kallisto/releases/tag/v0.52.0)
23. [Source](https://chanzuckerberg.com/eoss/proposals/)