CERI-KRISP/CholeraSeq is a Nextflow pipeline for data genomic analysis of Cholera outbreaks.
We have created a multi-fasta reference with global cohort available on NCBI, available at the link below.
The documentation for the pipeline is hosted at https://ceri-krisp.github.io/CholeraSeq/
A built-in test profile are available in the choleraseq pipeline with different size of datasets. This profile can be used to run tests on the relevant infrastructure using the test profile, to help users identify and resolve any infrastructural issue before the analysis stage.
NOTE: The snippets below assumes you have docker on the sever/machine you wish to test the pipeline. For other institutional configs please refer nf-core/configs project, which are all applicable to this pipeline.
$ nextflow run CERI-KRISP/CholeraSeq \
-profile test,docker --outdir test_output
For singularity please use the following command
$ nextflow run CERI-KRISP/CholeraSeq \
-profile test,singularity --outdir test_output
CERI-KRISP/CholeraSeq was originally written by the CholeraSeq publication authors.
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 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.