search

artic-network / artic-ncov2019

ARTIC nanopore protocol for nCoV2019 novel coronavirus
Creative Commons Attribution 4.0 International
168 stars 166 forks source link

Max of 400X #37

Closed charreca closed 3 years ago

charreca commented 4 years ago

Hi! We currently use ARTIC bioinformatics workflow to analyze raw nanopore SARS-CoV2 reads. We achieve a maximum of 400x coverage across regions with no overlapping amplicons for each sample. Is it normal to obtain a similar result for each sample? Is there a limit of depth that we can change in the pipeline? artic_example.pdf

Thanks for your answer,

Caroline

nickloman commented 4 years ago

This comes from the --normalise parameter: a value of 200 will give you 200x in each direction.

We have determined that adding more depth does not improve the results.

charreca commented 4 years ago

Ok many thanks for your answer. Just one additional question: what is the minimum of depth in your pipeline to call a consensus? For the others Illumina approaches the thereshold is usually set at 10X. With ONT approach, is it higher to overcome the higher error rate of nanopore sequencing?

Caroline

will-rowe commented 3 years ago

Hi @charreca. Sorry for only having seen this now.

The consensus sequence will be masked with Ns wherever a position has <20X depth of coverage. We also mask out positions where called variants have failed to pass the variant filters. Hope this helps. We have recently updated our documentation to give more detail on the pipeline. Please open a new issue in https://github.com/artic-network/fieldbioinformatics if you have any further questions.