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@ -485,6 +485,7 @@ NXF_OPTS='-Xms1g -Xmx4g'
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### Tutorial - How to create your custom database
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#### Kraken2
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Kraken2 allows the user to build custom databases.
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To install a taxonomy:
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@ -509,8 +510,8 @@ kraken2-build --add-to-library genome.fa --db $DBNAME
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You can follow Kraken2 [tutorial](https://github.com/DerrickWood/kraken2/blob/master/docs/MANUAL.markdown#custom-databases) for a more detailed description.
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#### Centrifuge
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Centrifuge allows the user to [build custom databases](https://ccb.jhu.edu/software/centrifuge/manual.shtml#custom-database). The user should download taxonomy files, make custom `seqid2taxid.map` and combine the fasta files together.
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```bash
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```
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#### Kaiju
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It is possible to [create custom databases](https://github.com/bioinformatics-centre/kaiju#custom-database) with Kaiju.
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```bash
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```
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#### MALT
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To create a custom database for MALT, the user should download and unzip the following database which lists all NCBI records. The input files are specified using -i and the index is specified using -d. A detailed description for each argument can be found [here](https://software-ab.informatik.uni-tuebingen.de/download/malt/manual.pdf)
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```bash
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```
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#### Bracken
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You can follow Bracken [tutorial](https://ccb.jhu.edu/software/bracken/index.shtml?t=manual) to build a custom database. Alternatively, you can use one of the indexes that can be found [here](https://benlangmead.github.io/aws-indexes/k2).
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#### KrakenUniq
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For KrakenUniq, we recommend using one of the available databases [here](https://benlangmead.github.io/aws-indexes/k2). But if you wish to build your own, please see the [documentation](https://github.com/fbreitwieser/krakenuniq/blob/master/README.md#custom-databases-with-ncbi-taxonomy).
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#### DIAMOND
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To create a custom database for DIAMOND, the user should download and unzip the NCBI's taxonomy files. The `makedb` needs to be executed afterwards. A detailed description can be found [here](https://github.com/bbuchfink/diamond/wiki/1.-Tutorial)
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```bash
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@ -566,6 +572,7 @@ rm *dmp *txt *gz *prt *zip
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```
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#### mOTUs
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A detailed description on how to download mOTUs database can be found [here](https://github.com/motu-tool/mOTUs)
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## Troubleshooting and FAQs
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