From 1eeb3b337aaa557e3278e86cd4f47bcfd2bc4879 Mon Sep 17 00:00:00 2001 From: Sofia Stamouli <91951607+sofstam@users.noreply.github.com> Date: Thu, 22 Dec 2022 11:07:09 +0100 Subject: [PATCH] Update usage.md --- docs/usage.md | 11 +++++------ 1 file changed, 5 insertions(+), 6 deletions(-) diff --git a/docs/usage.md b/docs/usage.md index e64726e..e51656d 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -474,19 +474,18 @@ You can follow Bracken [tutorial](https://ccb.jhu.edu/software/bracken/index.sht #### 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_012920.1 9606 NC_001134.8 4392 NC_001135.5 4392 +```bash +centrifuge-download -o taxonomy taxonomy + 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 ```