ahmedmagds/GNUVID: GNUVID v2.1: Globally circulating clonal complexes as of 2021-01-06 (Variants of Concern now being assigned)

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GNUVID 2.1 GNUVID now assigns the three new variants of concern (UK, SA and Brazilian):

CC81085 represents the Brazilian P.1 lineage (a.k.a. 20J/501Y.V3).
CC71014 represents the South African B.1.351 lineage (a.k.a. 20H/501Y.V2).
10 CCs represent the UK B.1.1.7 lineage (a.k.a. 20I/501Y.V1 Variant of Concern (VOC) 202012/01). (10 CCs: 46649, 45062, 49676, 54949, 54452, 58534, 57630, 66559, 62415 and 67441).

Globally circulating clonal complexes as of 2021-01-06:

159515 GISAID sequences have been included in this analysis.
GNUVID compressed the 1595150 ORFs in the 159515 genomes to 89491 unique alleles.
81097 Sequence Types (STs) have been assigned in this dataset and were clustered in 406 clonal complexes (CCs).
252 new CCs have been assigned.
133 CCs have been Inactive (i.e. Last time seen more than 1 month before 2021-01-06).
209 CCs have gone Quiet (i.e. Last seen 2-4 weeks before 2021-01-06).
64 CCs have been Active (i.e. Last seen within the 2 weeks before 2021-01-06).

GNUVID v2.2 now uses minimap2 and Gofasta to align to the reference for prediction using the random