New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Consequences of using vsearch on NovaSeq data #549
Comments
@slambrechts you probably refer to NovaSeq's simplified quality encoding. The short answer is: no known adverse effect yet. Only marginal effects are known. For instance, |
@frederic-mahe ok great, thank you for the info. If I understand correctly, there is also no need to adjust maxee for fastq filtering? |
Earlier this year, I've listed the following reduced sets of quality values (see issue #474):
These are subsets of usual quality sets, so I do not expect any particular difficulties for
When using I could be wrong though, please feel free to suggest tests or configurations. |
basic tests added to our test suite (frederic-mahe/vsearch-tests@bd064e7) |
Hi,
I know there are consequences of using dada2 on NovaSeq data (e.g. benjjneb/dada2#791), but do you know if there are similar problems with using vsearch on novaseq data?
Best,
Sam
The text was updated successfully, but these errors were encountered: