ahmedmagds/GNUVID: GNUVID 2.2

GNUVID v2.2 now uses minimap2 and Gofasta to align to the reference for prediction using the random forest classifier. GNUVID now assigns genomes to five new Variants of Concern:

• CC81085 represents the Brazilian P.1 lineage (a.k.a. 20J/501Y.V3).
• CC70949 represents the Brazilian P.2 lineage.
• CC72860 represents the Californian B.1.429 (CAL.20C) lineage.
• 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). ## New Features
• GNUVID now excludes genomes that does not pass quality check for sequence length (15000) and proportion of ambiguity (Ns) (0.5). User can change these cutoffs.
• Skip exact matching (-e): do only prediction [Default: do exact matching first].
• Prediction block size (-b): you can now assign the block size of genomes to be predicted at once [Default: 1000]. This will be helpful for machines with limited memory.