Introduction

nf-core/structure is a bioinformatics pipeline that prepares assembly data for a STRUCTURE bayesian clustering data using variant sites based on a reference. Note that it doesn't run the STRUCTURE analysis itself (yet) but rather prepare your data as an input of the tool.

1. Read .fna assembly data
2. Align fasta files against a reference (Minimap2)
3. Call variants with resulting alignment (bcftools)
4. Apply some filters to the resulting VCF file (vcftools)
5. Finally it converts the final file to a STRUCTURE like format (STRUCTURE)

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:

samplesheet.csv:

sample,fna_file_path
CONTROL_REP1,AEG588A1_S1_L002_R1_001.fna

Each row represents a sample with associated assembly information with .fna extension.

Now, you can run the pipeline using:

nextflow run nf-core/structure \
   -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 this github repository. For more details about the output files and reports, please refer to the output documentation.

Credits

nf-core/structure was originally written by Lucas Freitas.

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.

For further information or help, don't hesitate to get in touch on the Slack #structure 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.