Centrifuge for human host contamination

replikation / poreCov

SARS-CoV-2 workflow for nanopore sequence data

https://case-group.github.io/

GNU General Public License v3.0

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Centrifuge for human host contamination #39

Closed replikation closed 3 years ago

replikation commented 3 years ago

add some metrics for human host contamination check (e.g. centrifuge)
need to clip primers prior analysis

replikation commented 3 years ago

@hoelzer do you know which database you guys are using for this? i assume a DB with human AND the virus to allow for distinct classification between both (?)

hoelzer commented 3 years ago

@replikation yes correct!

4.3 Activating taxonomic Read Filtering If necessary, reads not derived from SARS-COV-2 can be excluded. Read classification is based on corresponding k-mer frequencies using a defined kraken2 database (--krakenDb). A pre-processed database containing SARS-CoV2 and human genome sequences can be downloaded from:

https://zenodo.org/record/3854856

see https://gitlab.com/RKIBioinformaticsPipelines/ncov_minipipe