From 98f3ab9fd1ba0e9a8c1bf5adcf5b5dd8bb7993f1 Mon Sep 17 00:00:00 2001 From: Sofia Stamouli Date: Fri, 9 Dec 2022 15:35:51 +0100 Subject: [PATCH] Apply prettier --- docs/usage.md | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/docs/usage.md b/docs/usage.md index 8f6d776..d17d168 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -484,15 +484,19 @@ NXF_OPTS='-Xms1g -Xmx4g' ### Tutorial - How to create your custom database #### Kraken2 + Kraken2 allows the user to build custom databases. You can follow Kraken2 [tutorial](https://github.com/DerrickWood/kraken2/blob/master/docs/MANUAL.markdown#custom-databases). #### Centrifuge + Centrifuge allows the user to [build custom databases](https://ccb.jhu.edu/software/centrifuge/manual.shtml#custom-database). #### Kaiju + It is possible to [create custom databases](https://github.com/bioinformatics-centre/kaiju#custom-database) with Kaiju. #### MALT + To create a custom database for MALT, the user should download and unzip the following database which lists all NCBI records. The input files are specified using -i and the index is specified using -d. A detailed description for each argument can be found [here](https://software-ab.informatik.uni-tuebingen.de/download/malt/manual.pdf) ```bash @@ -502,12 +506,15 @@ malt-build -i path/to/fasta/files/*.{fna,fa} -s DNA -d index -t 8 -st 4 -a2t meg ``` #### 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). #### KrakenUniq + For KrakenUniq, we recommend using one of the available databases [here](https://benlangmead.github.io/aws-indexes/k2) #### DIAMOND + To create a custom database for DIAMOND, the user should download and unzip the NCBI's taxonomy files. The `makedb` needs to be executed afterwards. A detailed description can be found [here](https://gensoft.pasteur.fr/docs/diamond/0.8.22/diamond_manual.pdf) ```bash @@ -524,6 +531,7 @@ rm *dmp *txt *gz *prt *zip ``` #### mOTUs + A detailed description on how to download mOTUs database can be found [here](https://github.com/motu-tool/mOTUs) ## Troubleshooting and FAQs