Hello. I’m new in the nexclade communities.
I didn’t found a proper documentation that explain how each result in the nexclade output is generated and what it represent ?
Specifically the parameters qc.overallScore and qc.overallStatus.
Can someone please paste me the link to this documentation (or explain me the parameters) ?
Cheers
Hi, in fact on clades.nextstrain.org they left the code in developper mode so we can debug it.
In run.ts they are computing all the SNP of your sequence,
the main point is that they are then calling
{ match, privateMutations } = treeFindNearestNodes({ analysisResult, rootSeq, auspiceData })
which means they are picking the closest node X in a global nextstrain tree (auspiceData). This closest node stuff is what you will see when clicking on ‘show tree’.
Then the score is computed in rulePrivateMutations.ts
totalNumberOfMutations =
privateMutations.length + insertions.length + deletions.length
score = (Math.max(0, totalNumberOfMutations - typical) * 100) / cutoff
where privateMutations are the SNP of your sequence relatively to the node X they found at the previous step, and typical = 5.
To summarize a 501Y.v2 sequence is expected to have no more than 5 more mutations than one of the main sublineages of 501Y.v2.
I didn’t check where they are taking in account the missing data (the NNNNN in the sequence).
Thanks for the explication of the clade assignment.
But I try to find the explication for the parameters qc.overallScore in the output of nexclade. Do you know that ?
Hello @nbargues , I replied on Github:
@babarlelephant, Nextclade is shipped in production mode, but we also enabled source maps , in case someone wanted to browse or debug the code. Looks like it is useful 
It is probably better to clone the code from Github, to setup the local copy of the application using developer’s guide and to study and modify the code in convenience of your favorite text editor.