Hi Shannon, yeah I’m curious because it looks very close to the Sierra Leone sequences, which is surprising, given that Liberian EBOV was not thought to have come from Sierra Leone. This is the first publicly released EBOV genome from Liberia (with the exception of KM251803, the small PCR fragment of the L gene from Nigeria ex Liberia). So before jumping to conclusions about country to country transmissions and rates of viral evolution, the question that comes to mind is how much the choice of reference might have influenced the final assembly, so it’d be helpful to see the raw read alignments against its own consensus. Are you up for sharing a BAM file?
I can work with you to try de novo assembly, but there’s a bunch of rough edges in our pipeline that make it harder to use (currently) outside our compute environment. I’m thinking within a few months, we’ll have those smoothed out. I can walk you through what is currently available (it’s quite messy at the moment), but if you’re okay with sharing reads, it may be faster if I give it a run myself and send you the resulting fastas and bams. You have my email address from your earlier visit, right?