Genotyping RSV samples from nanopore sequencing data
- minimap2
- samtools >= 1.10
- nextclade
- artic = 1.2.4
- medaka = 1.11.3
This package can be installed with its dependencies via bioconda.
conda install -c bioconda rsv-typer
To use the pipeline run the following command:
rsv-typer -i /path/to/reads -s sample_name -o /path/to/output/directory -m medaka_model
or
python3 /path/to/process_RSV_sample.py -i /path/to/reads -s sample_name -o /path/to/output/directory -m medaka_model
The input (-i) should consist of basecalled, demultiplexed nanopore sequencing reads that have passed the quality check.
The sample (-s) determines the prefix of the output directories within the given output directory.
The medaka model (-m) should be chosen according to the version of the basecaller used. For further information on medaka models see:
https://github.com/nanoporetech/medaka
The output will consist of five different directories containing the output of the different steps in the pipeline and a summary file in which the subtype, the reference file used for the artic pipeline and the genotype can be found. The generated consensus sequence can be found in the artic directory.