# "Rep82" reference genome database

## Summary

"Rep82" is a database of complete bacterial, archaeal and viral genomes based on NCBI RefSeq release 82.

## Inclusion criteria

Bacterial and archaeal genomes were selected based on the NCBI [manifest](ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/bacteria/assembly_summary.txt) file that was current at the time of RefSeq v82's release. Specifically, genomes marked as "reference genome" or "representative genome" in the column "refseq_category" were selected.

All viral genomes were included.

## Contents

The directory contains the following materials:

- Raw genome sequences in Fasta format
- Compatible NCBI taxonomy database (taxdump) and taxonomy mapping files
- **SHOGUN** database (with wrappers for Bowtie2, BURST and UTree) (tested with SHOGUN 1.0.5)
- **Bowtie2** database (tested with Bowtie2 2.3.4.1)
- **BURST** database (tested with BURST 0.99.7f)
- **UTree** database (tested with UTree 2.0RF)
- **Kraken** database (tested with Kraken 1.0)
- **Centrifuge** database (tested with Centrifuge 1.0.3)

## Contact

- Main PI: **Dan Knights** (dknights@umn.edu)
- Database structure and application in SHOGUN: **Gabe Al-Ghalith** (algh0022@umn.edu)
- General application in metagenomics: **Qiyun Zhu** (qiyunzhu@gmail.com)
- Application in Qiita: **Antonio Gonzalez** (antgonza@gmail.com)
- IT support: **Jeff Dereus** (jdereus@ucsd.edu)

## Citation

Hillmann B, Al-Ghalith GA, Shields-Cutler RR, Zhu Q, Gohl DM, Beckman KB, Knight R, Knights D. Evaluating the information content of shallow shotgun metagenomics. _MSystems_. 2018 Oct 30;3(6):e00069-18. [[link](https://msystems.asm.org/content/3/6/e00069-18)]