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add reference
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Jianshu Zhao committed Oct 24, 2022
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Expand Up @@ -101,7 +101,7 @@ cargo install archaea --features="annembed_openblas-system"

- Intel:
You can enable simd instruction with the feature hnsw_rs/simdeez_f.
Using openblas instead of intel-mkl you would run:
Using openblas instead of intel-mkl you would run:
```bash
cargo build --release --features="annembed_openblas-system" --features="hnsw_rs/simdeez_f"
```
Expand Down Expand Up @@ -139,4 +139,11 @@ We provide pre-built genome/proteome database graph file for bacteria/archaea, v
- Bacteria/archaea genomes are the newest version of GTDB database (https://gtdb.ecogenomic.org), which defines a bacterial speces at 95% ANI. Note that GSearch can also run for even higher resolution species database such as 99% ANI.
- Virus data base are based on the JGI IMG/VR database newest version (https://genome.jgi.doe.gov/portal/IMG_VR/IMG_VR.home.html), which also define a virus OTU (vOTU) at 95% ANI.
- Fungi database are based on the entire RefSeq fungal genomes (retrived via the MycoCosm website), we dereplicated and define a fungal speices at 99.5% ANI.
- All three pre-built databases are available here:http://enve-omics.ce.gatech.edu/data/gsearch
- All three pre-built databases are available here:http://enve-omics.ce.gatech.edu/data/gsearch



## References

1. Zhao, J.*, et al.* GSearch: Ultra-Fast and Scalable Microbial Genome Search by combining Kmer Hashing with Hierarchical Navigable Small World Graphs. *bioRxiv* 2022:2022.2010.2021.513218. [https://www.biorxiv.org/content/10.1101/2022.10.21.513218v1].

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