Consider replacing Gotoh alignment algorithm

As I've been working on #549 to add support for SARS-CoV-2 references, I've had some trouble with running out of memory. I think it's partly that I'm running on equipment with less memory than I usually use, and partly that the SARS-CoV-2 genome is longer than HIV or HCV. The specific step that I've had most trouble with is aligning two consensus sequences using our Gotoh algorithm, so maybe it's time to look at alternatives.

@jeff-k had suggested we move from Gotoh to BWA, and that project seems to have been superceded by minimap2. Experiment with these tools for aligning the SARS-CoV-2 consensus sequences, and then decide whether they are worth switching to.

Tasks

• Switch genome coverage plot from Gotoh to minimap2 (#480).
• Use the same minimap2 alignment to clip out gene regions. Tracked in issue #479.
• Review other uses of Gotoh, and decide whether they should be switched.

Start by reviewing the remaining uses of the Gotoh alignment algorithm in the MiCall codebase, then experiment with BWA and minimap2 on SARS-CoV-2 consensus sequences. Compare the alternatives for the affected alignment steps and document which uses, if any, should be switched.