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theiagen / public_health_bacterial_genomics

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Streptococcus pneumoniae subworkflow #117

Closed emmadoughty closed 1 year ago

emmadoughty commented 2 years ago

OM has requested a wf for Strep pneumo.

There is a specific request for this wf to include serotyping. I suggest using SeroBA which is available in a docker image from Staph-B or directly from the developers at Sanger.

There is also a population genomics typing scheme for Strep pneumo that types genomes into Global Pneumococcal Sequence Clusters (GPSC). This provides an "international genomic definition of pneumococcal lineages" (Global Pneumococcal Sequencing Project) that is important in pathogen surveillance and especially for analyzing mechanisms in vaccine escape. The typing approach can be undertaken using PopPUNK and reference files provided by the Global Pneumococcal Sequencing project- instructions here (lower part of page). I think PopPUNK is available in a docker image, however, recommended installation is via conda.

kapsakcj commented 2 years ago

Will be addressed via #141 😃

kapsakcj commented 1 year ago

addressed via #141 and will be enhanced via #149 . closing this issue since 141 has been merged into main