nf-core / createtaxdb

Parallelised and automated construction of metagenomic classifier databases of different tools

Introduction

nf-core/createtaxdb is a bioinformatics pipeline that constructs custom metagenomic classifier databases from the same input reference genome set for multiple classifiers and profilers in a highly automated and parallelised manner.

1. Prepares input FASTA files for building
2. Builds databases for:
   • Bracken
   • Centrifuge
   • DIAMOND
   • Kaiju
   • Kraken2
   • MALT

Usage

Note

If you are new to Nextflow and nf-core, please refer to this page on how to set-up Nextflow. Make sure to test your setup with -profile test before running the workflow on actual data.

Now, you can run the pipeline using:

nextflow run nf-core/createtaxdb \
   -profile <docker/singularity/.../institute> \
   --input samplesheet.csv \
   --outdir <OUTDIR>

Warning

Please provide pipeline parameters via the CLI or Nextflow -params-file option. Custom config files including those provided by the -c Nextflow option can be used to provide any configuration except for parameters; see docs.

For more details and further functionality, please refer to the usage documentation and the parameter documentation.

Pipeline output

To see the results of an example test run with a full size dataset refer to the results tab on the nf-core website pipeline page. For more details about the output files and reports, please refer to the output documentation.

Credits

nf-core/createtaxdb was originally written by James A. Fellows Yates, Joon Klaps, Alexander Ramos Díaz and the nf-core community.

We thank the following people for their extensive assistance in the development of this pipeline:

• Zandra Fagernäs for logo design

Contributions and Support

If you would like to contribute to this pipeline, please see the contributing guidelines.

For further information or help, don't hesitate to get in touch on the Slack #createtaxdb channel (you can join with this invite).

Citations

An extensive list of references for the tools used by the pipeline can be found in the CITATIONS.md file.

You can cite the nf-core publication as follows:

The nf-core framework for community-curated bioinformatics pipelines.

Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.

Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.