Galaxy |

ARTIC minion (version 1.2.3+galaxy0)

Input Read File:

Coverage normalisation depth:

Sample at most this number of reads per amplicon and strand. default=0 (use all reads)

Use bwa aligner:

Select a primer scheme from your history or use one from a tool data table?:

Screening files must be stored in the 'primer_scheme_bedfiles' tool data table

Primer Scheme:

Will you select a reference genome from your history or use a built-in reference?:

Using reference genome:

Select genome from the list

Medaka model:

Model string to pass to medaka (see https://github.com/nanoporetech/medaka#models)

ARTIC minion aligns Nanopore reads that were generated from a tiling amplicon library against a viral reference sequence. It generates a consensus fasta file and a vcf variant file.

This tool is configured to use the experimental 'medaka' variant caller and must be supplied with the name of a model file to use with 'medaka', see the medaka web page for details.

Note that you should choose an appropriate model for the medaka version used by ARTIC minion.

ARTIC version	medaka version
1.2.1	1.0.3
1.3.0-dev	1.2.3