disclaimer: I'm a JBrowse 2 developer

I think @GenoMax 's advice is good, you can align the contigs vs the reference as is. Then, you could use JBrowse 2 (https://jbrowse.org/jb2) to visualize those alignments. Minimap2 for example will output a PAF file, and JBrowse 2 can visualize PAF files in a "synteny style" view

Here is a basic set of command line steps you can use for setting this up

npm install -g @jbrowse/cli
jbrowse create newdir # folder containing jbrowse 2 html,js,css etc

# samtools faidx creates fasta index
samtools faidx ref.fa
samtools faidx contigs.fa 

# add-assembly will copy your ref fast to the newdir
jbrowse add-assembly ref.fa --out newdir --load copy
jbrowse add-assembly contigs.fa --out newdir --load copy

# run alignment, the -c adds CIGAR strings creating base level alignment
minimap2 -c ref.fa contigs.fa > comparison.paf

# add the paf file as a "synteny track" in jbrowse, the assemblyNames is flipped in order that the minimap2 command uses
jbrowse add-track comparison.paf --assemblyNames contigs,ref --out newdir --load copy

# load gene annotations perhaps for the reference genome
jbrowse add-track ref.gff --out newdir --load copy --assembly ref
# may not have them but can load annotations predicted on the contigs also
jbrowse add-track contigs.gff --out newdir --load copy --assembly contigs

# start a simple http server in the newdir folder
cd newdir
npx serve
# open up http://localhost:3000 in your web browser

If you don't want a web server, you can also use "JBrowse Desktop" which is just a installer you can run (https://jbrowse.org/jb2/download/) but the CLI with the web server is easier to illustrate in a short number of steps

Then you can get dotplots or 'synteny style' views like this https://jbrowse.org/jb2/docs/user_guides/linear_synteny_view/