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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Als antwoord op @sdwfrost
@ZaminIqbal Unless you expect some reads/regions to be highly divergent or have tricky indels, I'd expect mappers to be comparable1 antwoord 0 retweets 0 vind-ik-leuks -
Als antwoord op @dho @ZaminIqbal
we're using random primers and fishing out viral reads from the 99% human. Even slightly different SMALT settings matter...
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Als antwoord op @sdwfrost @ZaminIqbal
Have you first tried removing the human reads with
@K_G_Andersen and colleagues' viral-ngs filters? I'd do that first.2 antwoorden 0 retweets 0 vind-ik-leuks -
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...
2 antwoorden 0 retweets 2 vind-ik-leuks
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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