@niemasd @pvanheus Yes of course it is 😉 https://t.co/QDZgQePN1K
@BortzGroup @BrianRWasik @Virus_Evolution On benchmarking, one of my very favorite intrahost studies comes from @NathanGrubaugh et al. in @GenomeBiology (you may already be familiar). They also describe other approaches that may be of interest with Nanopor
An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar - PubMed https://t.co/NmttCredpA
9/ Within the same critique, the authors question why a 10x min coverage threshold was chosen, implying that a lower threshold (5x) is more appropriate. 10x (or more) is standard in viral genomics, e.g. the iVar Consensus default is 10 https://t.co/etEFSaB
@LabCflores @nanopore @illumina https://t.co/RkvZ8oOkCy https://t.co/3f6aY0AB18 Indeed it depends on viral load, sample quality, etc. Much better with Illumina, ideally two technical replicates.
RT @NathanGrubaugh: Interested in virus evolution or sequencing within host virus populations? Check out our latest in @GenomeBiology vali…
RT @BioMickWatson: An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar | Gen…
Primers are scored by blending the base penalty with a mismatch score calculated from the alignments to all other genomes. 3’ mismatches are more heavily penalised to fit with our observations from work with @NathanGrubaugh @K_G_Andersen https://t.co/9Byug
@arambaut @erikgarrison @mikegalla6 @NetworkArtic @mchugh_martin @Williams_T_C @bec_dewar @StefanRooke @AineToole @Scalene For those wanting to know, here is our paper showing that MinION + amplicon sequencing cannot accurately detect intahost variants. Co
@vscooper Also when evaluating intra-population genomics, as done in the companion paper (https://t.co/z8niuadkxS), I would argue the platform and method really does matter. SNV calling from tile-amplified genomes (as these maybe are?) is weird and full of
@nickdsandy @nanopore @aquaskyline Did you use strand bias as a feature? We have found it is highly discriminatory: https://t.co/uKp42GYfxV
An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar | Genome Biology | Full Text https://t.co/q9JrseRwQc
We investigated this here: https://t.co/TU50nCTtgC https://t.co/LfATjvrj60
RT @pathogenomenick: @ZaminIqbal @erikgarrison @MikeEberle @DNAmlin @ewanbirney If that's what you are after, the data from here might be u…
@ZaminIqbal @erikgarrison @MikeEberle @DNAmlin @ewanbirney If that's what you are after, the data from here might be useful: https://t.co/b18Rh1wFxw
RT @pathogenomenick: @ianholmes @mattloose @Clive_G_Brown @BenedictPaten @ewanbirney Rather difficult problem unless you have some clever n…
RT @pathogenomenick: @ianholmes @mattloose @Clive_G_Brown @BenedictPaten @ewanbirney Rather difficult problem unless you have some clever n…
RT @pathogenomenick: @ianholmes @mattloose @Clive_G_Brown @BenedictPaten @ewanbirney Rather difficult problem unless you have some clever n…
@ianholmes @mattloose @Clive_G_Brown @BenedictPaten @ewanbirney Rather difficult problem unless you have some clever new method to distinguish sequencing error from viral diversity... you might want to wait for nanopore's LCS/CCS protocol, or roll your own
An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar. https://t.co/uJIwFNjwNS
An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar. https://t.co/P4oUyFwmrj
RT @NathanGrubaugh: Interested in virus evolution or sequencing within host virus populations? Check out our latest in @GenomeBiology vali…
Check this out @PandoraIDNet! Such an interesting approach for us
RT @NathanGrubaugh: Interested in virus evolution or sequencing within host virus populations? Check out our latest in @GenomeBiology vali…
RT @NathanGrubaugh: Interested in virus evolution or sequencing within host virus populations? Check out our latest in @GenomeBiology vali…
RT @NathanGrubaugh: Interested in virus evolution or sequencing within host virus populations? Check out our latest in @GenomeBiology vali…
RT @NathanGrubaugh: Interested in virus evolution or sequencing within host virus populations? Check out our latest in @GenomeBiology vali…
RT @NathanGrubaugh: Interested in virus evolution or sequencing within host virus populations? Check out our latest in @GenomeBiology vali…
RT @NathanGrubaugh: Interested in virus evolution or sequencing within host virus populations? Check out our latest in @GenomeBiology vali…
RT @NathanGrubaugh: Interested in virus evolution or sequencing within host virus populations? Check out our latest in @GenomeBiology vali…
RT @NathanGrubaugh: Interested in virus evolution or sequencing within host virus populations? Check out our latest in @GenomeBiology vali…
RT @NathanGrubaugh: Interested in virus evolution or sequencing within host virus populations? Check out our latest in @GenomeBiology vali…
RT @NathanGrubaugh: Interested in virus evolution or sequencing within host virus populations? Check out our latest in @GenomeBiology vali…
RT @NathanGrubaugh: Interested in virus evolution or sequencing within host virus populations? Check out our latest in @GenomeBiology vali…
RT @NathanGrubaugh: Interested in virus evolution or sequencing within host virus populations? Check out our latest in @GenomeBiology vali…
@ISPM_ZOAP An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar. https://t.co/wlf6SZk38z
RT @NathanGrubaugh: Interested in virus evolution or sequencing within host virus populations? Check out our latest in @GenomeBiology vali…
RT @NathanGrubaugh: Interested in virus evolution or sequencing within host virus populations? Check out our latest in @GenomeBiology vali…
RT @NathanGrubaugh: Interested in virus evolution or sequencing within host virus populations? Check out our latest in @GenomeBiology vali…
RT @NathanGrubaugh: Interested in virus evolution or sequencing within host virus populations? Check out our latest in @GenomeBiology vali…
RT @NathanGrubaugh: Interested in virus evolution or sequencing within host virus populations? Check out our latest in @GenomeBiology vali…
RT @NathanGrubaugh: Interested in virus evolution or sequencing within host virus populations? Check out our latest in @GenomeBiology vali…
RT @NathanGrubaugh: Interested in virus evolution or sequencing within host virus populations? Check out our latest in @GenomeBiology vali…
RT @NathanGrubaugh: Interested in virus evolution or sequencing within host virus populations? Check out our latest in @GenomeBiology vali…
RT @NathanGrubaugh: Interested in virus evolution or sequencing within host virus populations? Check out our latest in @GenomeBiology vali…
RT @NathanGrubaugh: Interested in virus evolution or sequencing within host virus populations? Check out our latest in @GenomeBiology vali…
RT @NathanGrubaugh: Interested in virus evolution or sequencing within host virus populations? Check out our latest in @GenomeBiology vali…
RT @NathanGrubaugh: Interested in virus evolution or sequencing within host virus populations? Check out our latest in @GenomeBiology vali…
RT @annafagre: Super cool work by @NathanGrubaugh et al! https://t.co/rzsGyxQyGG
RT @NathanGrubaugh: Interested in virus evolution or sequencing within host virus populations? Check out our latest in @GenomeBiology vali…
RT @NathanGrubaugh: Interested in virus evolution or sequencing within host virus populations? Check out our latest in @GenomeBiology vali…
RT @NathanGrubaugh: Interested in virus evolution or sequencing within host virus populations? Check out our latest in @GenomeBiology vali…
RT @NathanGrubaugh: Interested in virus evolution or sequencing within host virus populations? Check out our latest in @GenomeBiology vali…
RT @NathanGrubaugh: Interested in virus evolution or sequencing within host virus populations? Check out our latest in @GenomeBiology vali…
Thread!
RT @NathanGrubaugh: Interested in virus evolution or sequencing within host virus populations? Check out our latest in @GenomeBiology vali…
RT @NathanGrubaugh: Interested in virus evolution or sequencing within host virus populations? Check out our latest in @GenomeBiology vali…
RT @NathanGrubaugh: Interested in virus evolution or sequencing within host virus populations? Check out our latest in @GenomeBiology vali…
RT @NathanGrubaugh: Interested in virus evolution or sequencing within host virus populations? Check out our latest in @GenomeBiology vali…
RT @annafagre: Super cool work by @NathanGrubaugh et al! https://t.co/rzsGyxQyGG
RT @NathanGrubaugh: Interested in virus evolution or sequencing within host virus populations? Check out our latest in @GenomeBiology vali…
RT @NathanGrubaugh: Interested in virus evolution or sequencing within host virus populations? Check out our latest in @GenomeBiology vali…
RT @NathanGrubaugh: Interested in virus evolution or sequencing within host virus populations? Check out our latest in @GenomeBiology vali…
Super cool work by @NathanGrubaugh et al!
In a method paper published in @GenomeBiology, @K_G_Andersen & colleagues describe an amplicon-based sequencing framework for accurately measuring intrahost virus diversity https://t.co/8gVhEdAPxw
RT @NathanGrubaugh: Interested in virus evolution or sequencing within host virus populations? Check out our latest in @GenomeBiology vali…
RT @NathanGrubaugh: Interested in virus evolution or sequencing within host virus populations? Check out our latest in @GenomeBiology vali…
RT @NathanGrubaugh: Interested in virus evolution or sequencing within host virus populations? Check out our latest in @GenomeBiology vali…
RT @NathanGrubaugh: Interested in virus evolution or sequencing within host virus populations? Check out our latest in @GenomeBiology vali…
RT @NathanGrubaugh: Interested in virus evolution or sequencing within host virus populations? Check out our latest in @GenomeBiology vali…
RT @NathanGrubaugh: Interested in virus evolution or sequencing within host virus populations? Check out our latest in @GenomeBiology vali…
RT @NathanGrubaugh: Interested in virus evolution or sequencing within host virus populations? Check out our latest in @GenomeBiology vali…
iVar: a method from @NathanGrubaugh, Gangavarapu, @K_G_Andersen and others, for using PrimalSeq to compare virus diversity between hosts https://t.co/DgFj7tqnDs
RT @NathanGrubaugh: Interested in virus evolution or sequencing within host virus populations? Check out our latest in @GenomeBiology vali…
RT @NathanGrubaugh: Interested in virus evolution or sequencing within host virus populations? Check out our latest in @GenomeBiology vali…
RT @NathanGrubaugh: Interested in virus evolution or sequencing within host virus populations? Check out our latest in @GenomeBiology vali…
Here's the readcube https://t.co/5snFUZtHqS
Interested in virus evolution or sequencing within host virus populations? Check out our latest in @GenomeBiology validating our amplicon-based NGS approach (PrimalSeq) and variant-calling software (iVar) for measuring within host virus diversity. https:
An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar https://t.co/L5TfNzytnR