diff --git a/docs/usage.md b/docs/usage.md index ccf2d85..4482778 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -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. An example of custom `seqid2taxid.map`: - -NC_001133.9 4392 -NC_012920.1 9606 -NC_001134.8 4392 -NC_001135.5 4392 +``` + NC_001133.9 4392 + NC_012920.1 9606 + NC_001134.8 4392 + NC_001135.5 4392 + ``` ```bash centrifuge-download -o taxonomy taxonomy