Description

SARS-CoV-2 genome clade assignment, mutation calling, and sequence quality checks (C++ implementation)

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

dataset (path)

Path containing the dataset files obtained by running nextclade dataset get

*

fasta (file)

FASTA file containing one or more consensus sequences

*.{fasta,fa}

Output

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

versions (file)

File containing software versions

versions.yml

csv (file)

CSV file containing nextclade results

*.{csv}

json (file)

JSON file containing nextclade results

*.{json}

json_tree (file)

Auspice JSON V2 containing nextclade results

*.{tree.json}

tsv (file)

TSV file containing nextclade results

*.{tsv}
included in
viralrecon
authors
Github user antunderwood Github user drpatelh
get in touch
Ask a question on Slack Open an issue on GitHub

Tools

nextclade
MIT

SARS-CoV-2 genome clade assignment, mutation calling, and sequence quality checks

github.com/nextstrain/nextclade