Assess artic protocol pipelines

PoonLab / gromstole

Quantifying SARS-CoV-2 VoCs from NGS data of wastewater samples

MIT License

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Assess artic protocol pipelines #1

Closed ArtPoon closed 2 years ago

ArtPoon commented 2 years ago

Nanopore SOP: https://artic.network/ncov-2019/ncov2019-bioinformatics-sop.html
what is the standard bioinformatic pipeline for Illumina data?

How much will we have to modify these existing pipelines to obtain frequency data of individual polymorphisms (substitutions, indels)?

ArtPoon commented 2 years ago

iVar seems to be popular for Illumina data: https://github.com/andersen-lab/ivar

ArtPoon commented 2 years ago

Need to adapt existing pipeline to record not only individual mutations, but also mutations observed in linkage in short reads - this will need some custom data structure

ArtPoon commented 2 years ago

See reading list