Introduction

nf-core/cap is a bioinformatics pipeline for Centromere Analysis in genomic assemblies. It identifies and characterizes centromeric regions using tandem repeat detection, machine learning-based prediction, and comprehensive genomic feature analysis. The pipeline accepts genome assemblies in FASTA format and produces publication-ready visualizations and annotations of centromeric regions.

The pipeline performs the following steps:

1. Dependency checking (nhmmer, mafft)
2. Tandem repeat detection (TRASH2)
3. Repeat classification and filtering
4. Optional: Transposable element annotation parsing (EDTA output)
5. Optional: Gene annotation parsing (Helixer output)
6. Centromeric scoring based on repeat families, GC content, and sequence complexity
7. Machine learning-based centromere prediction (XGBoost)
8. GC content and Context Tree Weighting (CTW) analysis
9. Generation of comprehensive visualizations and reports

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/cap \
   -profile <docker/singularity/conda/.../institute> \
   --assembly genome.fasta \
   --outdir <OUTDIR>

With optional annotations:

nextflow run nf-core/cap \
   -profile <docker/singularity/conda/.../institute> \
   --assembly genome.fasta \
   --te_gff EDTA.gff3 \
   --gene_gff helixer.gff \
   --templates custom_repeats.fasta \
   --cores 8 \
   --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/cap was originally written by Piotr Włodzimierz. Original repo is here.

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

Authors here

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 #cap 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.