# Velvet

> software

**Wikidata**: [Q123207513](https://www.wikidata.org/wiki/Q123207513)  
**Source**: https://4ort.xyz/entity/velvet-q123207513

## Summary
Velvet is software specifically designed for de novo assembly of short DNA sequence reads using de Bruijn graphs. It is a bioinformatics tool used to reconstruct genomes or transcripts from fragmented sequencing data.

## Key Facts
- **License**: GNU General Public License, version 2.0
- **Current Stable Version**: 1.2.10 (released July 5, 2018)
- **Website**: http://web.archive.org/web/20111118113047/http://www.ebi.ac.uk/~zerbino/velvet/ (English language)
- **Classification**: Software (instance_of)
- **Copyright Status**: Copyrighted
- **Core Description**: "Velvet: algorithms for de novo short read assembly using de Bruijn graphs"
- **Source Code Repository**: https://github.com/dzerbino/velvet
- **Research Resource Identifier (RRID)**: SCR_010755

## FAQs
### Q: What is Velvet used for?
A: Velvet is used for de novo assembly of short DNA sequence reads, meaning it helps reconstruct complete genomes or transcripts from fragmented sequencing data without needing a reference sequence.

### Q: Who uses Velvet?
A: Velvet is primarily used by bioinformaticians, computational biologists, and researchers in genomics and transcriptomics projects dealing with next-generation sequencing data.

### Q: Is Velvet free to use?
A: Yes, Velvet is open-source software distributed under the GNU General Public License, version 2.0.

## Why It Matters
Velvet was a groundbreaking tool in bioinformatics, addressing the critical challenge of assembling genomes from the short, error-prone reads produced by early next-generation sequencers. Its use of de Bruijn graphs for assembly significantly improved the accuracy and contiguity of assemblies compared to earlier methods. Velvet enabled researchers to tackle the genomes of complex organisms, facilitating advances across fields like evolutionary biology, medical research, and microbial ecology. By providing a robust and accessible algorithm, it accelerated the pace of genomics discovery and became a foundational tool in the field, particularly for de novo projects.

## Notable For
- **Pioneering Algorithm**: One of the first widely adopted tools to use de Bruijn graphs specifically for short-read assembly, significantly advancing the field.
- **Widespread Adoption**: Became a standard tool for de novo genome and transcriptome assembly from next-generation sequencing data, used in numerous published studies.
- **Open-Source Model**: Successfully maintained and developed as open-source software under the GPL v2.0, fostering community contribution and accessibility.
- **RRID Designation**: Recognized by the Research Resource Identification Initiative (RRID: SCR_010755) for its importance as a bioinformatics tool.
- **Longevity**: Demonstrated sustained utility and active development over many years, with the stable version (1.2.10) released in 2018.

## Body
### Overview and Purpose
Velvet is software dedicated to the computational process of *de novo* assembly of short DNA sequence reads generated by high-throughput sequencing technologies. Its primary function is to reconstruct original genomic or transcriptomic sequences from these fragmented pieces without relying on a pre-existing reference sequence. It specifically employs the de Bruijn graph algorithm, which efficiently breaks reads into shorter k-mers (subsequences of length k) and uses their overlaps to build a graph representing the original sequence.

### Technical Details and Algorithm
The core algorithm utilized by Velvet is the de Bruijn graph. This involves processing input short reads (typically from Illumina or similar sequencers) into k-mers. These k-mers are then used as nodes in a graph, with edges representing overlaps between k-mers. Velvet optimizes the graph through an iterative process involving error correction (consolidation) and graph simplification (unitigging and scaffolding) to produce contiguous sequence blocks (contigs) and longer scaffolds.

### Licensing and Accessibility
Velvet is distributed under the GNU General Public License, version 2.0 (GPLv2). This license ensures the software is free to use, modify, and distribute, with the requirement that any modifications or derived works also be licensed under GPLv2. The source code is publicly hosted on GitHub.

### Version History and Development
The stable version of Velvet is 1.2.10, released on July 5, 2018. This version was archived and tagged on GitHub. The software has a history of development, with earlier versions available, though the stable release v1.2.10 represents a significant milestone. The website hosted at the European Bioinformatics Institute (EBI) has been archived since 2011, reflecting its long-standing presence in the bioinformatics community.

### Source and Citation
The foundational work describing Velvet is published as "Velvet: algorithms for de novo short read assembly using de Bruijn graphs." This academic paper serves as the primary source detailing the algorithms and capabilities of the software. Velvet has also been assigned a Research Resource Identifier (RRID: SCR_010755) by the NIH.

## References

1. [Release 1.2.10. 2018](https://github.com/dzerbino/velvet/releases/tag/v1.2.10)