Reaching sequence divergence threshold where minimap2 will fail to align new sequences to reference

COG-UK / datapipe

Nextflow implementation of grapevine

GNU General Public License v3.0

8 stars 3 forks source link

Reaching sequence divergence threshold where minimap2 will fail to align new sequences to reference #14

Closed rmcolq closed 3 years ago

rmcolq commented 3 years ago

MSA currently generated via minimap2. We are approaching 15% sequence divergence from the reference so will need to update to use a panel of references for this

rmcolq commented 3 years ago

Add summaries to internal webhook to alarm if there is a large sequence drop out. Do both before/after pangolin step (has internal minimapping) and before/after alignment step.

Change asm5 to asm20 in minimap command