Improve documentation about input alignment

[ktmeaton]

More detail is needed to explain the input alignment (--alignment alignment.fasta)!

[anagrei]

Hi,
We now use rebar and were not sure why do you recommend: "Please note that the --alignment should be aligned to the same reference as in the dataset reference.fasta! We strongly recommend nextclade." into your examples from the docs.
We've made the aligment with Augur and got less novel recombinants compared to the output with Nextclade alignment. We thought the Augur alignment should be preferred as more accurate over the Nextclade alignment.
Is it OK to take the Augur alignment or there is a special reason to use the Nextclade alignment?

Thank you