Hello,

You can annotate your contigs and visualize from gbk file using

Python package : https://github.com/gamcil/clinker

or

R package: https://github.com/wilkox/gggenes

They can be used to visualize your contigs content

Best

Thank you so much for the suggestions Oscar!

However, I neither wish to annotate my contigs nor visualise the content of the contigs. I simply wish to align my FASTA contigs to a reference genome.

In that case you can use

UGene: http://ugene.net/

or

Jalview: https://www.jalview.org/

Best,