ALPINE (Anachronistic Lineage and Persistent INfection Explorer) 核心工具

请参阅这里原始的 ALPINE 工作流程仓库。此仓库包含正在开发的用于替换先前用 Julia 编写的 ALPINE 管道核心组件的 Rust 源代码。该工具具有丰富的命令行界面，旨在允许研究人员在没有调用整个 Nextflow 管道和相关 Docker 容器的情况下执行 ALPINE 类型的分析。

当你运行 alpine --help 时，出现的工具用法如下

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ALPINE: Anachronistic Lineage and Persistent INfection Explorer
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Command line interface for the core Rust components of ALPINE.
These commands are called in the full pipeline, which is imple-
mented in Nextflow alongside `seqkit`, `csvtk`, `nushell`,
`vsearch`, and a bin of bespoke Python scripts. However, users
may also use the commands available in this crate to run
similar analyses themselves via the command line.


Usage: alpine [OPTIONS] [COMMAND]

Commands:
  replace-gaps       Replace FASTA gap symbols '-' with masked bases 'N'.
  filter-by-n        Filter out FASTA records with more than the desired number of masked 'N' bases.
  separate-by-month  Use collection dates from FASTA record metadata to sort all FASTA records into a separate FASTA for each year-month combination.
  distance-matrix    Compute a symmetric pairwise distance matrix based on how dissimilar sequences in the provided FASTA are to one another.
  help               Print this message or the help of the given subcommand(s)

Options:
  -v, --verbose...         Increase logging verbosity
  -q, --quiet...           Decrease logging verbosity
  -t, --threads <THREADS>  [default: 3]
  -h, --help               Print help

要设置和尝试此工具集，可以安装 Rust 工具链并自行构建，或者在克隆到您的机器上的此目录后运行 ./easy_install。