# hifiasm

> software

**Wikidata**: [Q113018366](https://www.wikidata.org/wiki/Q113018366)  
**Source**: https://4ort.xyz/entity/hifiasm

## Summary
hifiasm is a software tool for haplotype-resolved de novo genome assembly using phased assembly graphs. It is specifically designed to assemble diploid genomes with accurate haplotype separation from long-read sequencing data.

## Key Facts
- hifiasm is classified as software.
- It is funded by the Chan Zuckerberg Initiative via the "Essential Open Source Software for Science program grant" (as of September 6, 2022).
- The software is described by the academic paper titled "Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm".
- It focuses on resolving haplotypes in diploid organisms during genome assembly.
- Its primary application involves long-read sequencing data for high-quality genome construction.

## FAQs
### Q: What problem does hifiasm solve?
A: hifiasm solves the challenge of assembling diploid genomes by accurately separating and reconstructing maternal and paternal haplotypes, which is critical for studies involving genetic variation and disease research.

### Q: Is hifiasm open source?
A: Yes, hifiasm is open-source software, as recognized by the Chan Zuckerberg Initiative's "Essential Open Source Software for Science" program grant.

### Q: What sequencing data does hifiasm work with?
A: hifiasm is optimized for long-read sequencing data, leveraging phased assembly graphs to resolve haplotypes in complex genomes.

## Why It Matters
Accurate haplotype resolution is fundamental to understanding genetic diversity, disease mechanisms, and evolutionary biology. Traditional assembly tools often collapse haplotypes, leading to fragmented and incomplete genome representations. hifiasm addresses this by using phased assembly graphs to maintain haplotype integrity during assembly, enabling researchers to construct high-quality, chromosome-level diploid genomes. This capability advances precision medicine, conservation genomics, and evolutionary studies by providing a more complete genetic blueprint of diploid organisms.

## Notable For
- Specializes in haplotype-resolved de novo assembly using phased assembly graphs.
- Recipient of a Chan Zuckerberg Initiative grant for "Essential Open Source Software for Science" (2022).
- Designed specifically for long-read sequencing data to resolve diploid genome complexity.
- Pioneers the integration of phased graphs in long-read assembly workflows.

## Body
### Overview
- hifiasm is a software tool for genomics research.
- It functions as a specialized genome assembler with a focus on diploid organisms.

### Development and Funding
- Funded by the Chan Zuckerberg Initiative.
- Grant received through the "Essential Open Source Software for Science program" (awarded September 6, 2022).
- Funding documented in the Chan Zuckerberg Initiative's EOSS proposals archive.

### Technical Purpose
- Engineered for haplotype-resolved de novo genome assembly.
- Utilizes phased assembly graphs to separate maternal and paternal haplotypes.
- Optimized for long-read sequencing data (e.g., PacBio or Oxford Nanopore).
- Addresses limitations in assembling diploid genomes with high heterozygosity.

### Recognition
- Acknowledged as essential open-source software in the genomic sciences.
- Described by the publication "Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm".
- Supports research requiring accurate haplotype reconstruction in complex genomes.

## References

1. [Source](https://chanzuckerberg.com/eoss/proposals/)