Description

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

Input

name:type
description
pattern

meta{:bash}

:map

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

fasta{:bash}

:file

FASTA file containing one or more consensus sequences

*.{fasta,fa}

dataset{:bash}

:directory

Path containing the dataset files obtained by running nextclade dataset get

*

Output

name:type
description
pattern

csv{:bash}

meta{:bash}

:map

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

${prefix}.csv{:bash}

:file

CSV file containing nextclade results

*.{csv}

csv_errors{:bash}

meta{:bash}

:map

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

${prefix}.errors.csv{:bash}

:file

CSV file containing errors from nextclade results

*.{errors.csv}

csv_insertions{:bash}

meta{:bash}

:map

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

${prefix}.insertions.csv{:bash}

:file

CSV file containing insertions from nextclade results

*.{insertions.csv}

tsv{:bash}

meta{:bash}

:map

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

${prefix}.tsv{:bash}

:file

TSV file containing nextclade results

*.{tsv}

json{:bash}

meta{:bash}

:map

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

${prefix}.json{:bash}

:file

JSON file containing nextclade results

*.{json}

json_auspice{:bash}

meta{:bash}

:map

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

${prefix}.auspice.json{:bash}

:file

Auspice JSON V2 containing nextclade results

*.{tree.json}

ndjson{:bash}

meta{:bash}

:map

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

${prefix}.ndjson{:bash}

:file

newline-delimited JSON file containing nextclade results

*.{ndjson}

fasta_aligned{:bash}

meta{:bash}

:map

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

${prefix}.aligned.fasta{:bash}

:file

FASTA file containing aligned sequences from nextclade results

*.{aligned.fasta}

fasta_translation{:bash}

meta{:bash}

:map

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

*_translation.*.fasta{:bash}

:file

FASTA file containing aligned peptides from nextclade results

*.{_translation.}*.{fasta}

nwk{:bash}

meta{:bash}

:map

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

${prefix}.nwk{:bash}

:file

NWK file containing nextclade results

*.{nwk}

versions{:bash}

versions.yml{:bash}

:file

File containing software versions

versions.yml

Tools

nextclade
MIT

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

github.com/nextstrain/nextclade
included in
viralrecon
maintainers
Github user antunderwood
Github user drpatelh
Github user drpatelh
get in touch
Ask a question on Slack Open an issue on GitHub