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NRLBM / assembly

Basic assembly workflow for NRLBM
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Add M1UK typing for S. pyogenes #12

Closed boasvdp closed 2 years ago

boasvdp commented 2 years ago

For Streptococcus pyogenes, we are interested in the M1UK lineage (first described here: ).

Add a functionality where the 27 lineage-specific SNPs are searched for all Spyo.

This should be implemented in the typing subworkflow. However, this implies that the typing should be done based on genome assembly rather than read mapping. Snippy supports contig shredding and mapping. Test whether this is sufficient to identify SNPs

boasvdp commented 2 years ago

Also check depth per SNP position? samtools depth

boasvdp commented 2 years ago

Added in https://github.com/NRLBM/assembly/commit/08580168638c7c15c61263c9f4885d4fff7817c0

SNP depth is not checked yet, may be future improvement