Skip to content
Permalink
Browse files

Update readme with new augur reqs

  • Loading branch information
trvrb committed Feb 13, 2020
1 parent d67d08b commit faa3c861dad678c591a44479792b0ef461f5c2cb
Showing with 2 additions and 4 deletions.
  1. +2 −4 README.md
@@ -52,10 +52,8 @@ with a [containerized Nextstrain installation](https://nextstrain.org/docs/getti

The resulting output JSON at `auspice/ncov.json` can be visualized by running `auspice view --datasetDir auspice` or `nextstrain view auspice/` depending on local vs containerized installation.

_This requires [Augur](https://github.com/nextstrain/augur) version >=6.2.0, released Jan 25, 2020._
_This requires [Augur](https://github.com/nextstrain/augur) version >=6.3.0, released Feb 13, 2020._

## Notes

There were apparently spurious SNPs present in the nCoV samples in the first and last few bases of the alignment that were masked as likely sequencing artifacts. A SNP at 18529 in BetaCoV/Wuhan/IVDC-HB-04/2020 appears directly adjacent to a long stretch of ambiguous bases and so has also been masked.

Site numbering and genome structure uses [BetaCoV/Wuhan-Hu-1/2019](https://www.ncbi.nlm.nih.gov/nuccore/MN908947) as reference. The phylogeny is rooted relative to early samples from Wuhan. Temporal resolution assumes a nucleotide substitution rate of 3 × 10^-4 subs per site per year. There were SNPs present in the nCoV samples in the first and last few bases of the alignment that were masked as likely sequencing artifacts. The sample Wuhan/IPBCAMS-WH-05/2020 has been dropped from the analysis due to the appearance of clustered, spurious SNPs.
Site numbering and genome structure uses [BetaCoV/Wuhan-Hu-1/2019](https://www.ncbi.nlm.nih.gov/nuccore/MN908947) as reference. The phylogeny is rooted relative to early samples from Wuhan. Temporal resolution assumes a nucleotide substitution rate of 5 × 10^-4 subs per site per year. There were SNPs present in the nCoV samples in the first and last few bases of the alignment that were masked as likely sequencing artifacts.

0 comments on commit faa3c86

Please sign in to comment.
You can’t perform that action at this time.