Introduction

sanger-tol/genomeprofiling is a bioinformatics pipeline that runs a series statistical analysis on a genome and its longread data.

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.

Due to the small amount of data required to run the pipeline, this pipeline does not accept a samplesheet as input.

Now, you can run the pipeline using:

nextflow run sanger-tol/genomeprofiling \
   -profile <docker/singularity/.../institute> \
   --sample TestRun \
   --input [genome1.fasta, genome2.fasta] \
   --longreads [longread1.fasta.gz, longread2.fasta.gz] \
   --kmer_length 31
   --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.

Credits

sanger-tol/genomeprofiling was originally written by DLBPointon.

Contributions and Support

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

Citations

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

This pipeline uses code and infrastructure developed and maintained by the nf-core community, reused here under the MIT license.

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.