mashtree:tldr:cef94

mashtree: Fastest method in mashtree to create a tree from fastq and/or fasta files using multiple threads, piping into a newick file.

mashtree

$ mashtree --numcpus ${12} ${*-fastq-gz} ${*-fasta} > ${mashtree-dnd}

try on your machine

The given command is using the tool "mashtree" to perform a specific task. Here is a breakdown of the command:

mashtree: This is the name of the tool or command that will be executed.
--numcpus: This flag is used to specify the number of CPUs (or cores) that should be used for the execution of the command. In this case, it is using the value of ${12} (which indicates the 12th command-line argument) as the number of CPUs to be used.
${*-fastq-gz}: This is a wildcard syntax used to match and include all command-line arguments ending with "-fastq-gz". The actual command-line arguments will depend on how the command is being executed and what data files are provided as inputs.
${*-fasta}: Similar to the previous wildcard syntax, this includes all command-line arguments ending with "-fasta".
>: This is a redirection operator used to redirect the output of the command to a file instead of printing it on the screen.
${mashtree-dnd}: This represents the name of the file where the output of the command will be saved. The actual file name will depend on the value assigned to ${mashtree-dnd}.

In summary, this command executes the "mashtree" tool using a specific number of CPUs and uses wildcard matching to include input files ending with "-fastq-gz" and "-fasta". The output of the command is then redirected to a file whose name is defined by ${mashtree-dnd}.

This explanation was created by an AI. In most cases those are correct. But please always be careful and never run a command you are not sure if it is safe.

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