Nextclade

note

Viral genome alignment, clade assignment, mutation calling, and quality checks.

https://github.com/nextstrain/nextclade

DOI: 10.21105/joss.03773

MIT License

Nextclade assigns input sequences to clades and lineages based on differences between the input sequences and Nextstrain reference sequences. In addition, it judges the validity of the samples by performing several quality control checks on the input sequences.

File search patterns

nextclade:
  contents: seqName;clade;
  num_lines: 1