# SeqKit

> toolkit for fasta and fastq manipulation

**Wikidata**: [Q115348765](https://www.wikidata.org/wiki/Q115348765)  
**Source**: https://4ort.xyz/entity/seqkit

## Summary
SeqKit is a cross-platform, ultrafast toolkit for manipulating FASTA and FASTQ files, widely used in bioinformatics. Written in Go, it provides efficient command-line utilities for processing biological sequence data.

## Key Facts
- **Purpose**: Toolkit for FASTA and FASTQ file manipulation in bioinformatics.
- **Programming Language**: Written in Go, a language developed by Google in 2009.
- **License**: Released under the MIT License.
- **Operating Systems**: Compatible with Linux, Microsoft Windows, and macOS.
- **First Release**: Version 0.1 was released on March 11, 2016.
- **Latest Version**: Version 2.3.1, released on September 22, 2022.
- **Source Code**: Hosted on GitHub at [https://github.com/shenwei356/seqkit](https://github.com/shenwei356/seqkit).
- **Website**: Official documentation available at [https://bioinf.shenwei.me/seqkit](https://bioinf.shenwei.me/seqkit).

## FAQs
### Q: What is SeqKit used for?
A: SeqKit is used for manipulating FASTA and FASTQ files, which are common formats in bioinformatics for storing sequence data. It provides tools for tasks like filtering, converting, and analyzing these files.

### Q: What programming language is SeqKit written in?
A: SeqKit is written in Go, a programming language known for its efficiency and cross-platform compatibility.

### Q: Is SeqKit free to use?
A: Yes, SeqKit is released under the MIT License, which allows for free use, modification, and distribution.

### Q: On which operating systems can SeqKit run?
A: SeqKit is compatible with Linux, Microsoft Windows, and macOS.

### Q: Where can I find the source code for SeqKit?
A: The source code for SeqKit is available on GitHub at [https://github.com/shenwei356/seqkit](https://github.com/shenwei356/seqkit).

## Why It Matters
SeqKit plays a crucial role in bioinformatics by providing a fast and efficient way to manipulate FASTA and FASTQ files. These files are fundamental in genomics and other biological research areas, often containing large datasets that require processing. SeqKit's cross-platform compatibility and ease of use make it accessible to researchers and practitioners across different operating systems. By offering a suite of command-line tools, SeqKit simplifies tasks such as sequence filtering, conversion, and analysis, thereby accelerating research workflows and reducing the time spent on data manipulation.

## Notable For
- **Cross-Platform Compatibility**: Runs on Linux, Microsoft Windows, and macOS.
- **Efficiency**: Written in Go, known for its performance and concurrency features.
- **Open Source**: Released under the MIT License, encouraging community contributions and modifications.
- **Versatility**: Offers a wide range of utilities for FASTA and FASTQ file manipulation.
- **Active Development**: Regular updates and releases, with the latest version being 2.3.1 as of September 22, 2022.

## Body
### Overview
SeqKit is a toolkit designed for the manipulation of FASTA and FASTQ files, which are standard formats in bioinformatics for storing nucleotide and protein sequences. It provides a collection of command-line utilities that facilitate various operations on these files, such as filtering, converting, and analyzing sequence data.

### Development and Release
SeqKit was first released on March 11, 2016, with version 0.1. Since then, it has undergone numerous updates, with the latest version being 2.3.1, released on September 22, 2022. The toolkit is actively maintained and updated, with a history of regular releases.

### Technical Details
- **Programming Language**: SeqKit is written in Go, a programming language developed by Google in 2009. Go is known for its efficiency, concurrency features, and cross-platform compatibility.
- **License**: SeqKit is released under the MIT License, which allows for free use, modification, and distribution.
- **Operating Systems**: SeqKit is compatible with Linux, Microsoft Windows, and macOS, making it accessible to a wide range of users.

### Features and Utilities
SeqKit offers a variety of utilities for FASTA and FASTQ file manipulation, including:
- **Filtering**: Removing or selecting sequences based on various criteria.
- **Conversion**: Converting between different file formats.
- **Analysis**: Performing statistical analyses on sequence data.
- **Manipulation**: Modifying sequence data in various ways.

### Source Code and Documentation
The source code for SeqKit is hosted on GitHub at [https://github.com/shenwei356/seqkit](https://github.com/shenwei356/seqkit). The official documentation is available at [https://bioinf.shenwei.me/seqkit](https://bioinf.shenwei.me/seqkit), providing detailed information on installation, usage, and available utilities.

## Schema Markup
```json
{
  "@context": "https://schema.org",
  "@type": "Thing",
  "name": "SeqKit",
  "description": "A cross-platform and ultrafast toolkit for FASTA/Q file manipulation.",
  "url": "https://bioinf.shenwei.me/seqkit",
  "sameAs": ["https://www.wikidata.org/wiki/Q107420055"],
  "additionalType": "Software"
}

## References

1. [Source](https://github.com/shenwei356/seqkit/releases/tag/v2.3.1)
2. [Source](https://github.com/shenwei356/seqkit/releases/tag/v2.3.0)
3. [Release 0.1. 2016](https://github.com/shenwei356/seqkit/releases/tag/v0.1)
4. [Release 0.1.1. 2016](https://github.com/shenwei356/seqkit/releases/tag/v0.1.1)
5. [Release 0.1.2. 2016](https://github.com/shenwei356/seqkit/releases/tag/v0.1.2)
6. [Release 0.1.3. 2016](https://github.com/shenwei356/seqkit/releases/tag/v0.1.3)
7. [Release 0.1.3.1. 2016](https://github.com/shenwei356/seqkit/releases/tag/v0.1.3.1)
8. [Release 0.1.4. 2016](https://github.com/shenwei356/seqkit/releases/tag/v0.1.4)
9. [Release 0.1.4.1. 2016](https://github.com/shenwei356/seqkit/releases/tag/v0.1.4.1)
10. [Release 0.1.5. 2016](https://github.com/shenwei356/seqkit/releases/tag/v0.1.5)
11. [Release 0.1.5.1. 2016](https://github.com/shenwei356/seqkit/releases/tag/v0.1.5.1)
12. [Release 0.1.5.2. 2016](https://github.com/shenwei356/seqkit/releases/tag/v0.1.5.2)
13. [Release 0.1.6. 2016](https://github.com/shenwei356/seqkit/releases/tag/v0.1.6)
14. [Release 0.1.7. 2016](https://github.com/shenwei356/seqkit/releases/tag/v0.1.7)
15. [Release 0.1.8. 2016](https://github.com/shenwei356/seqkit/releases/tag/v0.1.8)
16. [Release 0.1.9. 2016](https://github.com/shenwei356/seqkit/releases/tag/v0.1.9)
17. [Release 0.2.0. 2016](https://github.com/shenwei356/seqkit/releases/tag/v0.2.0)
18. [Release 0.2.1. 2016](https://github.com/shenwei356/seqkit/releases/tag/v0.2.1)
19. [Release 0.2.2. 2016](https://github.com/shenwei356/seqkit/releases/tag/v0.2.2)
20. [Release 0.2.3. 2016](https://github.com/shenwei356/seqkit/releases/tag/v0.2.3)
21. [Release 0.2.4. 2016](https://github.com/shenwei356/seqkit/releases/tag/v0.2.4)
22. [Release 0.2.4.1. 2016](https://github.com/shenwei356/seqkit/releases/tag/v0.2.4.1)
23. [Release 0.2.5. 2016](https://github.com/shenwei356/seqkit/releases/tag/v0.2.5)
24. [Release 0.2.5.1. 2016](https://github.com/shenwei356/seqkit/releases/tag/v0.2.5.1)
25. [Release 0.2.6. 2016](https://github.com/shenwei356/seqkit/releases/tag/v0.2.6)
26. [Release 0.2.7. 2016](https://github.com/shenwei356/seqkit/releases/tag/v0.2.7)
27. [Release 0.2.8. 2016](https://github.com/shenwei356/seqkit/releases/tag/v0.2.8)
28. [Release 0.2.9. 2016](https://github.com/shenwei356/seqkit/releases/tag/v0.2.9)
29. [Release 0.3.0. 2016](https://github.com/shenwei356/seqkit/releases/tag/v0.3.0)
30. [Release 0.3.1. 2016](https://github.com/shenwei356/seqkit/releases/tag/v0.3.1)
31. [Release 0.3.1.1. 2016](https://github.com/shenwei356/seqkit/releases/tag/v0.3.1.1)
32. [Release 0.3.2. 2016](https://github.com/shenwei356/seqkit/releases/tag/v0.3.2)
33. [Release 0.3.3. 2016](https://github.com/shenwei356/seqkit/releases/tag/v0.3.3)
34. [Release 0.3.4. 2016](https://github.com/shenwei356/seqkit/releases/tag/v0.3.4)
35. [Release 0.3.4.1. 2016](https://github.com/shenwei356/seqkit/releases/tag/v0.3.4.1)
36. [Release 0.3.5. 2016](https://github.com/shenwei356/seqkit/releases/tag/v0.3.5)
37. [Release 0.3.6. 2016](https://github.com/shenwei356/seqkit/releases/tag/v0.3.6)
38. [Release 0.3.7. 2016](https://github.com/shenwei356/seqkit/releases/tag/v0.3.7)
39. [Release 0.3.8. 2016](https://github.com/shenwei356/seqkit/releases/tag/v0.3.8)
40. [Release 0.3.8.1. 2016](https://github.com/shenwei356/seqkit/releases/tag/v0.3.8.1)
41. [Release 0.3.9. 2016](https://github.com/shenwei356/seqkit/releases/tag/v0.3.9)
42. [Release 0.4.0. 2016](https://github.com/shenwei356/seqkit/releases/tag/v0.4.0)
43. [Release 0.4.1. 2016](https://github.com/shenwei356/seqkit/releases/tag/v0.4.1)
44. [Release 0.4.2. 2016](https://github.com/shenwei356/seqkit/releases/tag/v0.4.2)
45. [Release 0.4.3. 2016](https://github.com/shenwei356/seqkit/releases/tag/v0.4.3)
46. [Release 0.4.4. 2017](https://github.com/shenwei356/seqkit/releases/tag/v0.4.4)
47. [Release 0.4.5. 2017](https://github.com/shenwei356/seqkit/releases/tag/v0.4.5)
48. [Release 0.5.0. 2017](https://github.com/shenwei356/seqkit/releases/tag/v0.5.0)
49. [Release 0.5.1. 2017](https://github.com/shenwei356/seqkit/releases/tag/v0.5.1)
50. [Release 0.5.2. 2017](https://github.com/shenwei356/seqkit/releases/tag/v0.5.2)