File: nextclade.md

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---
name: Nextclade
url: https://github.com/nextstrain/nextclade
description: Viral genome alignment, clade assignment, mutation calling, and quality checks
---

Nextclade assigns input sequences to SARS-Cov-2 clades based on differences between the input sequences and [Nextstrain](https://nextstrain.org/) reference sequences. In addition, it judges the validity of the samples by performing several quality control checks on the input sequences.