Nanopore reads

[AkshitaJain2709]

Can I use this software on an already assembled partial mitogenome. The genome was sequenced as metagenomic environmental sample using Oxford Nanopore long read technology. Any help is appreciated

[linzhi2013]

MitoZ is not a reference-based assembler.

(1) assemble your NGS reads with MitoZ directly.
(2) you can map your NGS reads to your ref mitogenome and call consensus
(3) use MitoBim or similar tools

[AkshitaJain2709]

I have a partial mitogenome extracted from my metagenome data, can i then run MitoZ on that sequence to visualise my mitogenome?

[linzhi2013]

I have a partial mitogenome extracted from my metagenome data, can i then run MitoZ on that sequence to visualise my mitogenome?

for visualization, MitoZ asks for a GenBank file as input.

You can use the annotate subcommand to annotate your mitogenome, so you will get a GenBank file.

[AkshitaJain2709]

hello, thanks for your reply.

I annotated my mitogenome using the script provided however, it doesn't code for any tRNA genes.
I then used another web based tool called MITOS2 (Galaxy), and that is encoding for tRNA genes in the same mitogenome.
I am now not sure which annotation is accurate. Could you please let me know if I need to turn on any dependencies to encode for tRNAs.
Thanks