nextclade
Nextclade is a command line tool used for viral genome analysis. It is specifically designed to work with SARS-CoV-2, the virus responsible for COVID-19. Nextclade allows researchers and scientists to compare and analyze the genetic sequences of different strains of the virus. The tool provides insights into the mutation patterns, genetic diversity, and potential variants of SARS-CoV-2. Nextclade is developed to be user-friendly, with intuitive command line interface and clear instructions. It utilizes advanced bioinformatics algorithms and data analysis techniques to process and interpret genomic data. The software can handle large datasets efficiently, making it suitable for analyzing numerous viral genomes simultaneously. Nextclade has various features, including sequence alignment, identification of mutations, and annotation of important genetic features. The tool also incorporates a quality control mechanism to ensure the accuracy and reliability of the results. It supports multiple input formats and allows users to customize analysis parameters, providing flexibility in analysis workflows.
List of commands for nextclade:
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nextclade:tldr:33d3d nextclade: Try reverse complement if sequence does not align.$ nextclade run --retry-reverse-complement -d ${dataset_name} -t ${path-to-output_tsv} ${path-to-input_fasta}try on your machineexplain this command
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nextclade:tldr:4f277 nextclade: Use a downloaded [D]ataset, producing all [O]utputs.$ nextclade run -D ${path-to-dataset_dir} -O ${path-to-output_dir} ${path-to-dataset_dir-sequences-fasta}try on your machineexplain this command
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nextclade:tldr:53055 nextclade: List all available datasets.$ nextclade dataset listtry on your machineexplain this command
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nextclade:tldr:7464c nextclade: Download the latest SARS-CoV-2 dataset.$ nextclade dataset get --name sars-cov-2 --output-dir ${path-to-directory}try on your machineexplain this command
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nextclade:tldr:cfe7d nextclade: Create a TSV report, auto-downloading the latest [d]ataset.$ nextclade run -d ${dataset_name} ${path-to-fasta} -t ${path-to-output_tsv}try on your machineexplain this command