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@ -474,19 +474,18 @@ 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). 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. 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. You need four components: 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. An example of custom `seqid2taxid.map`:
```bash
centrifuge-download -o taxonomy taxonomy
## custom seqid2taxid.map
NC_001133.9 4392 NC_001133.9 4392
NC_012920.1 9606 NC_012920.1 9606
NC_001134.8 4392 NC_001134.8 4392
NC_001135.5 4392 NC_001135.5 4392
```bash
centrifuge-download -o taxonomy taxonomy
cat *.{fa,fna} > input-sequences.fna cat *.{fa,fna} > input-sequences.fna
centrifuge-build -p 4 --conversion-table seqid2taxid.map --taxonomy-tree taxonomy/nodes.dmp --name-table taxonomy/names.dmp input-sequences.fna taxprofiler_cf centrifuge-build -p 4 --conversion-table seqid2taxid.map --taxonomy-tree taxonomy/nodes.dmp --name-table taxonomy/names.dmp input-sequences.fna taxprofiler_cf
``` ```