jannikseidelqbic/nf-core-detaxizer

A pipeline to check for certain taxa in fastq files and optionally filter out this taxonomic group

Introduction

nf-core/detaxizer is a bioinformatics pipeline that 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 quality assessment via FastQC and optional preprocessing (adapter trimming, quality cutting and optional length and quality filtering) using fastp, followed by taxon classification with kraken2 and/or bbduk, and optionally 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 bbduk in the classification and/or the validation step, fasta files for usage of bbduk and creating the blastn database to verify the targeted taxon.

1. Read QC (FastQC)
2. Optional pre-processing (fastp)
3. Classification of reads (Kraken2, and/or bbduk)
4. Optional validation of searched taxon/taxa (blastn)
5. Optional filtering of the searched taxon/taxa from the reads (either from the raw files or the preprocessed reads, using either the output from the classification (kraken2 and/or bbduk) or blastn)
6. Summary of the processes (how many were classified and optionally how many were validated)
7. Present QC for raw reads (MultiQC)

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.

First, prepare a samplesheet with your input data that looks as follows:

sample,short_reads_fastq_1,short_reads_fastq_2,long_reads_fastq_1
CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz,AEG588A1_S1_L002_R3_001.fastq.gz

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. For more detailed information about the samplesheet, see the usage documentation.

Note

Be aware that the tax2filter (default Homo sapiens) has to be in the provided kraken2 database (if kraken2 is used) and that the reference for bbduk (provided by the fasta_bbduk parameter) should contain the taxa to filter/assess if it is wanted to assess/remove the same taxa as in tax2filter. This overlap in the databases is not checked by the pipeline. To filter out/assess taxa with bbduk only, the tax2filter parameter is not needed but a fasta file with references of these taxa has to be provided.

Now, you can run the pipeline using:

nextflow run nf-core/detaxizer \
   -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/detaxizer was originally written by Jannik Seidel at the Quantitative Biology Center (QBiC).

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

• Daniel Straub

This work was initially funded by the German Center for Infection Research (DZIF).

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 #detaxizer channel (you can join with this invite).

Citations

If you use nf-core/detaxizer for your analysis, please cite it using the following doi: 10.5281/zenodo.10877147

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.