Coronavirus Disease Research Community - COVID-19

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Published July 20, 2021 | Version v2.3
Software Open

ahmedmagds/GNUVID: GNUVID v2.3

Creators

  • 1. Children's Hospital of Philadelphia

Description

  • 999,106 High Quality GISAID sequences have been included in this analysis from a total of 2,012,563 sequences.
  • GNUVID compressed the 9991060 ORFs in the 999106 genomes to 549768 unique alleles.
  • 523727 Sequence Types (STs) have been assigned in this dataset and were clustered in 2888 clonal complexes (CCs).
  • GNUVID now reports the WHO Naming system for VOCs/VOIs (e.g. Alpha, Beta..etc) as per the WHO updated on 07/06/2021.
  • GNUVID now excludes genomes that does not pass quality check for sequence length (20000) and proportion of ambiguity (Ns) (0.3). User can change these cutoffs.
  • A table showing summary information of the 177 Active Clonal Complexes (CCs) can be found here. A full report for the 2888 CCs can be found here

Files

ahmedmagds/GNUVID-v2.3.zip

Files (33.3 MB)

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Additional details

Related works

Is supplement to
https://github.com/ahmedmagds/GNUVID/tree/v2.3 (URL)