nextclade 命令

常用示例

说明

nextclade analyzes viral genome sequences, assigning clades, calling mutations, and assessing sequence quality. It's widely used for SARS-CoV-2 surveillance. The tool aligns sequences against a reference genome, identifies mutations (substitutions, insertions, deletions), and assigns sequences to clades in the phylogenetic tree. Quality control metrics flag potential problems: missing data, mixed bases, frameshifts, stop codons, and unusual mutations. These help identify sequencing errors or contamination. Datasets contain reference sequences, gene annotations, and clade definitions. Pre-built datasets are available for major pathogens. Custom datasets can be created. Output includes detailed mutation lists, clade assignments, and quality scores. Results can be visualized or processed for epidemiological analysis. Tree placement shows where sequences fit in the global phylogeny, useful for tracking outbreak origins.

参数

run

Analyze sequences.

dataset list

List available datasets.

dataset get

Download dataset.

-i _FILE_

Input FASTA file.

-d _NAME_

Dataset name.

-D _DIR_

Dataset directory.

-o _FILE_

Output TSV file.

--output-tree _FILE_

Output tree JSON.

--output-fasta _FILE_

Output aligned FASTA.

--output-json _FILE_

Output JSON results.

-j _N_

Number of threads.

--min-length _N_

Minimum sequence length.

--include-reference

Include reference in outputs.