From 29978d83b9177942c00d89b175f39053c99aa39c Mon Sep 17 00:00:00 2001
From: Sofia Stamouli <91951607+sofstam@users.noreply.github.com>
Date: Thu, 22 Dec 2022 11:03:49 +0100
Subject: [PATCH] Update centrifuge section

---
 docs/usage.md | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/docs/usage.md b/docs/usage.md
index 7b451e7..e64726e 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -474,7 +474,9 @@ 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). 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
 centrifuge-download -o taxonomy taxonomy