I have prepared a pairwise genome alignment pipeline for Nextflow and plan to submit it to nf-core as a standalone pipeline or a subworkflow.
Using tools from the LAST suite, it takes genomes in FASTA format, trains itself to find the best alignment parameters, aligns the genomes, reduces the result to a set one-to-one matches and produces a dotplot. Alignment files and dotplots for the intermediate steps (many-to-many and one-to-many) are also provided. It can align many query genomes to a single target genome (the one that will be indexed) in parallel.
I use it routinely on small genomes and trust it. If you find it useful or find issues, I would welcome your comments.
Readers in the future, please note that the URL will eventually change when the pipeline will be finalised.