folkehelseinstituttet/viralseq is a bioinformatics pipeline used at the Norwegian Institute of Public Health that is designed for highly variable viruses, and viruses that are likely to appear as co-infections between multiple strains, such as Hepatitis C Virus. The pipeline will identify the most likely major and minor strain in a sample sequenced with the Illumina platform. It will map the reads to these references using Bowtie2 and create consensus sequences. For Hepatitis C Viruses the pipeline can also run a GLUE-analysis to identify drug resistance mutations. maps Illumina reads to a reference genome and creates a consensus sequence.
The pipeline only requires Nextflow and Docker in order to run. Note that you must be able to run Docker as a non-root user as described here.
To run a minimal test:
nextflow run folkehelseinstituttet/viralseq/main.nf -r master -profile docker,test_illumina
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.