mashtree:tldr:87cfc
The given command, "mashtree --mindepth ${0} --numcpus ${12} ${-fastq-gz} ${-fasta} > ${mashtree-dnd}", is a command-line instruction that performs a specific task using the "mashtree" utility or program.
Here is the breakdown of the command:
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"mashtree": This is the name of the utility or program being executed. It is likely a bioinformatics tool used for phylogenetic analysis or comparing microbial genomes.
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"--mindepth ${0}": This is an option provided to the "mashtree" program. "--mindepth" is used to specify the minimum read depth for including a sample in the analysis. The value for this option is provided using the "${0}" variable.
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"--numcpus ${12}": Another option provided to the "mashtree" program. "--numcpus" allows you to specify the number of CPUs or processor cores to be used for the analysis. The value for this option is provided using the "${12}" variable.
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"${-fastq-gz}": Using "${-fastq-gz}", the command expects files in the current directory whose names end with "-fastq-gz" extension. This is likely the input file(s) in compressed FASTQ format containing genetic sequence data.
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"${*-fasta}": Similarly, this part of the command expects files in the current directory whose names end with "-fasta" extension. These are likely the input file(s) in FASTA format containing genetic sequence data.
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"> ${mashtree-dnd}": The ">" symbol is used for output redirection. In this case, any output generated by the "mashtree" program will be saved to a file named "mashtree-dnd". The "${mashtree-dnd}" variable holds the name of the output file.
To summarize, this command is running the "mashtree" program with some specified options (--mindepth and --numcpus) and input data files (-fastq-gz and -fasta), and redirecting the program's output to a file named "mashtree-dnd". The specific values for the options and files are expected to be provided through variables (e.g., ${0} and ${12}).