Dear Tweeps, does anyone know of the most sensitive read mapper for hepatitis B virus sequences before we start epic benchmarking exercise?
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Have you first tried removing the human reads with
@K_G_Andersen and colleagues' viral-ngs filters? I'd do that first.
Mapper? My go to is always Novoalign - can be tweaked to work for most viruses.
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Don't really like commercial stuff. I begrudgingly accept that the read mapper in CLC works really well...
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Commercial, yes, but free version great. I battled with this too, but it's the best and that's most important.
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