# Salmon

> read allignment tool

**Wikidata**: [Q112974082](https://www.wikidata.org/wiki/Q112974082)  
**Source**: https://4ort.xyz/entity/salmon-q112974082

## Summary
Salmon is a bioinformatics software tool designed for read alignment and transcript quantification. It provides fast and bias-aware quantification of transcript expression, making it valuable for analyzing RNA sequencing data in biological research.

## Key Facts
- Salmon is a software tool used for read alignment and transcript quantification in the field of bioinformatics
- It is developed by Rob Patro, Carl Kingsford, and Rafael Irizarry
- The tool is funded by the Chan Zuckerberg Initiative through the Essential Open Source Software for Science program grant (awarded in 2022)
- Salmon is licensed under GNU General Public License, version 3.0
- It is available on the website https://combine-lab.github.io/salmon/ with source code at https://github.com/COMBINE-lab/salmon
- The software has undergone multiple versions since 2015, with the earliest being version 0.4.1 released on June 11, 2015
- As of 2017, the latest version was 0.8.1 released on March 6, 2017

## FAQs
### Q: What is Salmon used for in bioinformatics?
A: Salmon is used for read alignment and transcript quantification. It provides fast and bias-aware quantification of transcript expression, making it a valuable tool for analyzing RNA sequencing data.

### Q: Who created the Salmon software?
A: Salmon was created by Rob Patro, Carl Kingsford, and Rafael Irizarry, who are the listed developers of the tool.

### Q: Is Salmon free to use?
A: Yes, Salmon is open-source software licensed under GNU General Public License, version 3.0, which means it is free to use, modify, and distribute.

### Q: When was Salmon first released?
A: The first version of Salmon, version 0.4.1, was released on June 11, 2015.

## Why It Matters
Salmon plays a crucial role in the field of bioinformatics by providing researchers with a fast and accurate tool for quantifying transcript expression from RNA sequencing data. Its bias-aware algorithms address common challenges in transcript quantification, leading to more reliable biological insights. As an open-source tool, it has democratized access to sophisticated bioinformatics analysis, allowing researchers with varying computational resources to perform high-quality transcriptomic analyses. The tool has become a standard in many RNA-seq pipelines, significantly contributing to the advancement of gene expression studies and understanding of biological processes.

## Notable For
- Being a widely adopted tool in bioinformatics for transcript quantification
- Its speed and efficiency in processing RNA sequencing data
- Addressing bias in transcript quantification, which is a common challenge in the field
- Receiving funding from the Chan Zuckerberg Initiative's Essential Open Source Software for Science program

## Body
### Overview
Salmon is a bioinformatics software tool that specializes in read alignment and transcript quantification. It is designed to analyze RNA sequencing data efficiently and accurately.

### Development and Team
Salmon is developed by Rob Patro, Carl Kingsford, and Rafael Irizarry. The tool is maintained by the COMBINE Lab, as indicated by its GitHub repository URL.

### Funding
Salmon received financial support from the Chan Zuckerberg Initiative through the Essential Open Source Software for Science program grant. This funding was provided in 2022 and specifically supports open-source software that is essential for scientific research.

### Licensing and Distribution
Salmon is distributed under the GNU General Public License, version 3.0. This open-source license allows users to freely use, modify, and distribute the software.

### Version History
Salmon has undergone continuous development since its initial release:
- Version 0.4.1 (released June 11, 2015)
- Version 0.4.2 (released June 15, 2015)
- Version 0.5.0 (released October 10, 2015)
- Version 0.5.1 (released November 13, 2015)
- Version 0.6.0 (released January 1, 2016)
- Version 0.7.0 (released August 15, 2016)
- Version 0.7.1 (released August 22, 2016)
- Version 0.7.2 (released August 31, 2016)
- Version 0.8.0 (released January 23, 2017)
- Version 0.8.1 (released March 6, 2017)

### Functionality
Salmon provides fast and bias-aware quantification of transcript expression. Its primary uses include read alignment and transcript quantification, making it a valuable tool for researchers working with RNA sequencing data.

### Accessibility and Resources
The tool is accessible through its official website (https://combine-lab.github.io/salmon/) and its source code repository (https://github.com/COMBINE-lab/salmon). These resources provide documentation, downloads, and updates for users and developers.

## References

1. [Source](https://combine-lab.github.io/salmon/contact/)
2. [Release 0.4.1. 2015](https://github.com/COMBINE-lab/salmon/releases/tag/v0.4.1)
3. [Release 0.4.2. 2015](https://github.com/COMBINE-lab/salmon/releases/tag/v0.4.2)
4. [Release 0.5.0. 2015](https://github.com/COMBINE-lab/salmon/releases/tag/v0.5.0)
5. [Release 0.5.1. 2015](https://github.com/COMBINE-lab/salmon/releases/tag/v0.5.1)
6. [Release 0.6.0. 2016](https://github.com/COMBINE-lab/salmon/releases/tag/v0.6.0)
7. [Release 0.7.0. 2016](https://github.com/COMBINE-lab/salmon/releases/tag/v0.7.0)
8. [Release 0.7.1. 2016](https://github.com/COMBINE-lab/salmon/releases/tag/v0.7.1)
9. [Release 0.7.2. 2016](https://github.com/COMBINE-lab/salmon/releases/tag/v0.7.2)
10. [Release 0.8.0. 2017](https://github.com/COMBINE-lab/salmon/releases/tag/v0.8.0)
11. [Release 0.8.1. 2017](https://github.com/COMBINE-lab/salmon/releases/tag/v0.8.1)
12. [Release 0.8.2. 2017](https://github.com/COMBINE-lab/salmon/releases/tag/v0.8.2)
13. [Release 0.9.0. 2017](https://github.com/COMBINE-lab/salmon/releases/tag/v0.9.0)
14. [Release 0.9.1. 2017](https://github.com/COMBINE-lab/salmon/releases/tag/v0.9.1)
15. [Release 0.10.0. 2018](https://github.com/COMBINE-lab/salmon/releases/tag/v0.10.0)
16. [Release 0.10.1. 2018](https://github.com/COMBINE-lab/salmon/releases/tag/v0.10.1)
17. [Release 0.10.2. 2018](https://github.com/COMBINE-lab/salmon/releases/tag/v0.10.2)
18. [Release 0.11.0. 2018](https://github.com/COMBINE-lab/salmon/releases/tag/v0.11.0)
19. [Release 0.11.1. 2018](https://github.com/COMBINE-lab/salmon/releases/tag/v0.11.1)
20. [Release 0.11.2. 2018](https://github.com/COMBINE-lab/salmon/releases/tag/v0.11.2)
21. [Release 0.11.3. 2018](https://github.com/COMBINE-lab/salmon/releases/tag/v0.11.3)
22. [Release 0.12.0. 2018](https://github.com/COMBINE-lab/salmon/releases/tag/v0.12.0)
23. [Release 0.13.0. 2019](https://github.com/COMBINE-lab/salmon/releases/tag/v0.13.0)
24. [Release 0.13.1. 2019](https://github.com/COMBINE-lab/salmon/releases/tag/v0.13.1)
25. [Release 0.14.0. 2019](https://github.com/COMBINE-lab/salmon/releases/tag/v0.14.0)
26. [Release 0.14.1. 2019](https://github.com/COMBINE-lab/salmon/releases/tag/v0.14.1)
27. [Release 0.14.2. 2019](https://github.com/COMBINE-lab/salmon/releases/tag/v0.14.2)
28. [Release 1.0.0. 2019](https://github.com/COMBINE-lab/salmon/releases/tag/v1.0.0)
29. [Release 1.1.0. 2019](https://github.com/COMBINE-lab/salmon/releases/tag/v1.1.0)
30. [Release 1.2.0. 2020](https://github.com/COMBINE-lab/salmon/releases/tag/v1.2.0)
31. [Release 1.2.1. 2020](https://github.com/COMBINE-lab/salmon/releases/tag/v1.2.1)
32. [Release 1.3.0. 2020](https://github.com/COMBINE-lab/salmon/releases/tag/v1.3.0)
33. [Release 1.4.0. 2020](https://github.com/COMBINE-lab/salmon/releases/tag/v1.4.0)
34. [Release 1.5.1. 2021](https://github.com/COMBINE-lab/salmon/releases/tag/v1.5.1)
35. [Release 1.5.2. 2021](https://github.com/COMBINE-lab/salmon/releases/tag/v1.5.2)
36. [Release 1.6.0. 2021](https://github.com/COMBINE-lab/salmon/releases/tag/v1.6.0)
37. [Release 1.7.0. 2022](https://github.com/COMBINE-lab/salmon/releases/tag/v1.7.0)
38. [Release 1.8.0. 2022](https://github.com/COMBINE-lab/salmon/releases/tag/v1.8.0)
39. [Release 1.9.0. 2022](https://github.com/COMBINE-lab/salmon/releases/tag/v1.9.0)
40. [Release 1.10.0. 2023](https://github.com/COMBINE-lab/salmon/releases/tag/v1.10.0)
41. [Release 1.10.1. 2023](https://github.com/COMBINE-lab/salmon/releases/tag/v1.10.1)
42. [Release 1.11.0. 2026](https://github.com/COMBINE-lab/salmon/releases/tag/v1.11.0)
43. [Release 1.11.1. 2026](https://github.com/COMBINE-lab/salmon/releases/tag/v1.11.1)
44. [Release 1.11.2. 2026](https://github.com/COMBINE-lab/salmon/releases/tag/v1.11.2)
45. [Release 1.11.3. 2026](https://github.com/COMBINE-lab/salmon/releases/tag/v1.11.3)
46. [Release 1.11.4. 2026](https://github.com/COMBINE-lab/salmon/releases/tag/v1.11.4)
47. [Source](https://chanzuckerberg.com/eoss/proposals/)