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  Sequence FASTA files are often passed as arguments to commandline tools. For example FASTA files can be passed as an argument to bowtie2-build to be indexed as an alignment reference \cite{langmead2012fast} or passed to trimmomatic as adapters to detect sequencing artifacts. The output filename used by Fast-O-Matic varies to reflect the reformatting performed. For seamless integration into automated workflows Fasta-O-Matic returns the full path of the new properly formatted FASTA file or the original file (if it is already formatted properly). This can be captured as a variable and used as an argument in subsequent commands. The Bash commands below show and example of capturing the FASTA file name as a variable.  Code : (backslashes are used to indicate a new line that is for display in the  article rather than the new lines being included in the actual code):  \begin{verbatim}  filename="$(python fasta_o_matic.py -f NC_010473_mock_scaffolds.fna \  -o ~/out_fasta_o_matic -c)" echo $filename  \end{verbatim}   
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