snakemake pipelines to run all the funky funcs
-
Import CoG-UK consensus fasta file
-
Clean and filter
-
Align to reference
-
Lineage type using PANGOLIN
-
Merge with GISAID alignment
-
Split into lineages of approximately equal size - A, B, B.1
-
Build IQ-Tree maximum likelihood trees for each
iqtree -m GTR+G -nt AUTO -czb -bb 1000 -s <sequences.fasta>
uses
iq-brownieto maintain taxon names unscathed
-
Clip out UK clusters using
cluster-funk -
Build report
-
trotters up