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updated wordlist
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mattheww95 committed Jul 22, 2024
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2 changes: 2 additions & 0 deletions .wordlist.txt
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gc
https
genotypic
bioinformatic
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2 changes: 1 addition & 1 deletion README.md
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- [GTDB Mash Sketch](https://zenodo.org/record/8408361): required for speciation and determination if sample is metagenomic
- [Decontamination Index](https://zenodo.org/record/8408557): Required for decontamination of reads (it is simply a minimap2 index)
- [Kraken2 nt database](https://benlangmead.github.io/aws-indexes/k2): Required for binning of metagenommic data and is an alternative to using Mash for speciation
- [Kraken2 nt database](https://benlangmead.github.io/aws-indexes/k2): Required for binning of metagenomic data and is an alternative to using Mash for speciation
- [Bakta database](https://zenodo.org/record/7669534): Running Bakta is optional and there is a light database option, however the full one is recommended. You will have to unzip and un-tar the database for usage. You can skip running Bakta however making the requirement of downloading this database **optional**.
- [StarAMR database](https://github.com/phac-nml/staramr#database-build): Running StarAMR is optional and requires downloading the StarAMR databases. Also if you wish to avoid downloading the database, the container for StarAMR has a database included which mikrokondo will default to using if one is not specified making this requirement **optional**.

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