Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of viral pathogens of concern, especially SARS-CoV-2
Wow this one is long overdue to address since it initially cropped up in April...
I'll document the proposed solution that has resolved false frameshifts in consensus assemblies generated by TheiaCov_ONT (v2.2.0) across at least one GridION seq run with 52 samples affected.
Re-assemble genomes using existing TheiaCov_ONT workflow w/ updated medaka model:r941_min_hac_variant_g507 ← model used by epi2me/wf-artic nextflow workflow
r941_min_hac_g507 ← model we advised to use previously
The _variant family is the set which is appropriate for the purposes of calling variants from reads aligned to a reference sequence. The non-_variant models are used for polishing draft assemblies and are not intended for calling variants. This is why wf-artic restricts the choice to the _variant family.
Currently, this solution will only apply to TheiaCov_ONT users that are using Nanopore sequencing (i.e. non-ClearLabs)
This does not include TheiaCov_ClearLabs/ClearLabs platform users because the Guppy version utilized in the platform is older than Guppy 5.0.7, so this medaka model will not be appropriate. CL users should continue to utilize the assemblies generated by the CL BIP workflow
Wow this one is long overdue to address since it initially cropped up in April...
I'll document the proposed solution that has resolved false frameshifts in consensus assemblies generated by TheiaCov_ONT (v2.2.0) across at least one GridION seq run with 52 samples affected.
Re-assemble genomes using existing TheiaCov_ONT workflow w/ updated medaka model:
r941_min_hac_variant_g507
← model used byepi2me/wf-artic
nextflow workflowr941_min_hac_g507
← model we advised to use previouslyAccording to ONT:
Currently, this solution will only apply to TheiaCov_ONT users that are using Nanopore sequencing (i.e. non-ClearLabs)
This does not include TheiaCov_ClearLabs/ClearLabs platform users because the Guppy version utilized in the platform is older than Guppy 5.0.7, so this medaka model will not be appropriate. CL users should continue to utilize the assemblies generated by the CL BIP workflow