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Jan 26, 2024
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Include a pre-built kaiju indexes in tutorial.md #440

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Include a pre-built kaiju indexes in tutorial.md
Joon-Klaps Jan 26, 2024
1e1c9aa
update changelog.md
Joon-Klaps Jan 26, 2024
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2 changes: 2 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -7,6 +7,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

### `Added`

- [#440](https://github.com/nf-core/taxprofiler/pull/440) Include pre-built kaiju databases in tutorial.md (added by @Joon-Klaps)

### `Fixed`

### `Dependencies`
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4 changes: 3 additions & 1 deletion docs/usage/tutorials.md
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Expand Up @@ -346,7 +346,9 @@ A detailed description can be found [here](https://github.com/bbuchfink/diamond/

### Kaiju custom database

To build a kaiju database, you need three components: a FASTA file with the protein sequences, the NCBI taxonomy dump files, and you need to define the uppercase characters of the standard 20 amino acids you wish to include.
A number of kaiju pre-built indexes for reference datasets are maintained by the the developers of kaiju and made available on the [kaiju website](https://bioinformatics-centre.github.io/kaiju/downloads.html). These databases can directly be used to run the workflow with Kaiju.

In case the databases above do not contain your desired libraries, you can build a custom kaiju database. To build a kaiju database, you need three components: a FASTA file with the protein sequences, the NCBI taxonomy dump files, and you need to define the uppercase characters of the standard 20 amino acids you wish to include.

:::warning
The headers of the protein fasta file must be numeric NCBI taxon identifiers of the protein sequences.
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