A pipeline to check for certain taxa in fastq files and optionally filter out this taxonomic group
nf-core/detaxizer is a bioinformatics pipeline that initially checks for the presence of a specific taxon in (meta)genomic fastq files and offers the option to filter out this taxon or taxonomic subtree. The process begins with preprocessing using fastp and quality assessment via FastQC, followed by taxon classification with kraken2 (the kraken2 database can be changed), and employs blastn for validation of the reads associated with the identified taxa. Users must provide a samplesheet to indicate the fastq files and, if utilizing the validation step, a fasta file for creating the blastn database to verify the targeted taxon.
- Read QC (
- Pre-processing (
- Classification of reads (
- Optional validation of searched taxon/taxa (
- Optional filtering of the searched taxon/taxa from the reads (either from the raw files or the preprocessed reads, using either the output from kraken2 or blastn)
- Summary of the processes
- Present QC for raw reads (
First, prepare a samplesheet with your input data that looks as follows:
Each row represents a fastq file (single-end) or a pair of fastq files (paired end). A third fastq file can be provided if long reads are present in your project. If you only have long reads put the reference to your file(s) in the forth column, leaving column 2 and 3 empty.
Now, you can run the pipeline using:
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;
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.
We thank the following people for their extensive assistance in the development of this pipeline:
Contributions and Support
If you would like to contribute to this pipeline, please see the contributing guidelines.
An extensive list of references for the tools used by the pipeline can be found in the
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.