nextstrain调试记录

[anneng]

nextstrain的架构：

[anneng]

安装
conda create -n nextstrain -c bioconda nextstrain-cli --yes
conda install -c conda-forge mamba --yes
conda activate nextstrain

mamba install -c conda-forge -c bioconda augur auspice nextalign snakemake git --yes
nextstrain check-setup --set-default

[anneng]

https://terra.bio/workflow-updates-to-the-covid-19-workspace-better-viral-assembly-and-phylogenetics-with-nextstrain/

[anneng]

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8237802/
Augur: a bioinformatics toolkit for phylogenetic analyses of human pathogens
nextstrain的流程部分使用了SnakeMake

[anneng]

https://terra.bio/workflow-updates-to-the-covid-19-workspace-better-viral-assembly-and-phylogenetics-with-nextstrain/

terra对nextstrain的支持