nextclade: first stab at nextclade genome dataset#48
Draft
Conversation
genehack
approved these changes
Sep 5, 2025
| The reference tree used in this dataset includes sequences for the 28 reference strains, along with (nearly) complete genomes of other representative strains for most genotypes. | ||
| This dataset can be used to assign genotypes to any sequence that includes at least 400 bp of the N450 region, including whole genome sequences. | ||
| In addition, this dataset implements simple quality control metrics based to the amount of missing sequence, the number of ambiguous nucleotides, frameshifts or stop codons, and clusters of mutations relative to sequences in the reference tree. | ||
| The reference tree used in this dataset includes uses a complete rubella virus genome, whole the nomenclature by the WHO is typically defined based on the E1 segment. |
Contributor
There was a problem hiding this comment.
Suggested change
| The reference tree used in this dataset includes uses a complete rubella virus genome, whole the nomenclature by the WHO is typically defined based on the E1 segment. | |
| The reference tree used in this dataset includes uses a complete rubella virus genome, while the nomenclature by the WHO is typically defined based on the E1 segment. |
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
2 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
This uses the measles full genome workflow as a template for rubella.