From 1eb3da758b04893fbe2199d8873cad461fc6308b Mon Sep 17 00:00:00 2001 From: Sofia Stamouli <91951607+sofstam@users.noreply.github.com> Date: Tue, 13 Dec 2022 09:38:09 +0100 Subject: [PATCH] Apply review suggestion Co-authored-by: James A. Fellows Yates --- docs/usage.md | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/docs/usage.md b/docs/usage.md index 6c1214d..c45d828 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -568,8 +568,12 @@ See the [MALT manual](https://software-ab.informatik.uni-tuebingen.de/download/m #### Bracken -You can follow Bracken [tutorial](https://ccb.jhu.edu/software/bracken/index.shtml?t=manual) to build a custom database. Alternatively, you can use one of the indexes that can be found [here](https://benlangmead.github.io/aws-indexes/k2). +Bracken does not provide any default databases for profiling, but rather building upon Kraken2 databases. See [Kraken2](#kraken2) for more information on how to build these. +In addition to a Kraken2 database, you also need to have the (average) read lengths (in bp) of your sequencing experiment, the K-mer size used to build the Kraken2 database, and Kraken2 available on your machine. + +```bash +bracken-build -d -k -l #### KrakenUniq For KrakenUniq, we recommend using one of the available databases [here](https://benlangmead.github.io/aws-indexes/k2). But if you wish to build your own, please see the [documentation](https://github.com/fbreitwieser/krakenuniq/blob/master/README.md#custom-databases-with-ncbi-taxonomy).