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Add new line in the description of custom file

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Sofia Stamouli 2023-01-19 13:44:10 +01:00 committed by GitHub
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@ -470,11 +470,12 @@ You can follow Bracken [tutorial](https://ccb.jhu.edu/software/bracken/index.sht
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. 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.
An example of custom `seqid2taxid.map`: An example of 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 ```bash
centrifuge-download -o taxonomy taxonomy centrifuge-download -o taxonomy taxonomy