-
Post-basecalling analysis for the mpox virus
The wf-mpx workflow provides a basic analysis of mpox sequencing data whether targeted or metagenomics.
This workflow can be performed on commandline or through EPI2ME Labs, giving users basic QC tools, a draft consensus sequence for review, a draft assembly and SNP context.
Please note, the workflow does not perform adapter or primer trimming. This means if targeted protocols are used, there could be artefacts at these sites.
-
Post-basecalling analysis for viral metagenomics
Please note that Oxford Nanopore Technologies does not currently offer a dedicated workflow for viral metagenomics analysis, meaning users will need to use or adapt third-party tools suitable for this application. However, we do offer a wf-metagenomics workflow but requires users to specify a custom database e.g. Kraken2 Metagenomic Virus Database.
For general post-basecalling data analysis options, please see the list below:
1. EPI2ME platform
The EPI2ME platform is a cloud-based data analysis service developed by Metrichor Ltd., a subsidiary of Oxford Nanopore Technologies. The EPI2ME platform offers a range of analysis workflows, e.g. for metagenomic identification, barcoding, alignment, and structural variant calling. The FastQ WIMP (Human + Viral) workflow compares sequence reads against a comprehensive corpus of virus genome sequences. This can be used to assign sequence reads to known viruses or to provide taxonomic hints for novel virus sequences that may be detected from metagenomics samples. The analysis requires no additional equipment or compute power, and provides an easy-to-interpret report with the results. For instructions on how to run an analysis workflow in EPI2ME, please follow the instructions in the EPI2ME protocol, beginning at the "Starting data analysis" step.
2. EPI2ME Labs tutorials and workflows
For more in-depth data analysis, Oxford Nanopore Technologies offers a range of bioinformatics tutorials and workflows available in EPI2ME Labs, which are available in the EPI2ME Labs section of the Community. The platform provides a vehicle where workflows deposited in GitHub by our Research and Applications teams can be showcased with descriptive texts, functional bioinformatics code and example data.
For identifying viral sequence reads from metagenomic samples, we would recommend our wf-metagenomics workflow. This nextflow-based analysis pipeline uses the kraken2 software to assign sequence reads to an organism (or virus) of origin. The bracken software considers the kraken2 results and prepares a quantitative view of the species observed within a metagenomic sample. A few different databases suitable for this workflow are maintained by the author and are publicly available at the Kraken 2 and Bracken indexes page.
3. Research analysis tools
Oxford Nanopore Technologies' Research division has created a number of analysis tools, which are available in the Oxford Nanopore GitHub repository. The tools are aimed at advanced users, and contain instructions for how to install and run the software. They are provided as-is, with minimal support.
The marine phage scripts repository includes a collection of python scripts that have been used in the recovery, identification and annotation of marine virus genomes from metagenomic samples. The scripts available here could be further adapted for more general viral metagenomic requirements.
4. Community-developed analysis tools
If a data analysis method for your research question is not provided in any of the resources above, please refer to the Bioinformatics section of the Resource centre. Numerous members of the Nanopore Community have developed their own tools and pipelines for analysing nanopore sequencing data, most of which are available on GitHub. Please be aware that these tools are not supported by Oxford Nanopore Technologies, and are not guaranteed to be compatible with the latest chemistry/software configuration.