Augur alignment failing - problem with mafft

[rneher]

I wrote a quick summary on how to switch to nextalign:

Avoiding large memory requirements by switching to `nextalign`

By default, Nextstrain’s pipeline to analyze SARS-CoV-2 uses mafft with the options --addfragments --keeplength to align all input sequences to the reference genome. For large data sets (>500k) this requires a lot of memory. To keep running the pipeline on the entire data set, we now use nextalign instead of mafft. The reduces the memory requirements to a few Gb and is faster than mafft. To use nextalign in your own workflow with the ncov workflow, you need to set two variables in your paramet…