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Update centrifuge section

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Sofia Stamouli 2022-12-22 11:03:49 +01:00 committed by GitHub
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@ -474,7 +474,9 @@ You can follow Bracken [tutorial](https://ccb.jhu.edu/software/bracken/index.sht
#### Centrifuge custom database #### Centrifuge custom database
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. Centrifuge allows the user to [build custom databases](https://ccb.jhu.edu/software/centrifuge/manual.shtml#custom-database). You need four file: a tab-separated file mapping sequence IDs to taxonomy IDs (`--conversion-table`), a \t|\t-separated file mapping taxonomy IDs to their parents and rank, up to the root of the tree (`--taxonomy-tree`), a '|'-separated file mapping taxonomy IDs to a name (`--name-table`) and the reference sequences.
The user should download taxonomy files, make custom `seqid2taxid.map` and combine the fasta files together.
```bash ```bash
centrifuge-download -o taxonomy taxonomy centrifuge-download -o taxonomy taxonomy