Nanopore seqeuencing analysis


I have nanopore sequencing results and I am trying to do variant calling using “Medaka tools” on galaxy yet I wanted to double check If I am doing it the right way or not

I initially use the medaka consensus tool to generate the H5 file:

  1. The input is a bam file that I obtained from aligning the fastq file via minimap2
  2. I select then the r941_min_high_g360 model since I am using a GridION and Guppy version 4.3.4
  3. I am not sure if I should set a read group, set a tag name and value before I execute or not? and I have noticed that there is no RG in the sorted bam file that I have as an input so, is it essential to add read group, set a tag name and value?

Then I use the generated H5 file to do the VC via the medaka variant tool using the human reference genome, I select annotated VCF and I select the bam to annotate the VCF is the same bam that I have used initially in the consensus tool


Welcome, @Maroismail!

Maybe you can get some insight from the workflows at NanoGalaxy

DE KONING, Willem et al. NanoGalaxy: Nanopore long-read sequencing data analysis in Galaxy. GigaScience, v. 9, n. 10, p. giaa105, 2020.