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\subsection{Customizing FASTA files to ensure that information is properly interpreted by downstream tools}  Regardless of whether a FASTA file is technically improperly formatted or it's format merely violates a popular convention convention,  it is critical to quality analysis workflows that data is converted into a format that will be correctly interpreted by downstream tools. Formatting issues can fall into multiple categories including actual format errors and formats that are not technically wrong but are non-standard that cause some tools to throw an error. Some format errors indicate a major problem like an attempt to use the wrong data format (e.g. the first line is not a FASTA header because it does not begin with a \verb|>| character). These types of errors will be subsequently referred to as fatal. Alternately, some formatting issues occur commonly without indicating the FASTA file is corrupt (e.g. improperly wrapped/unwrapped sequence lines, missing final new line characters, unusual new line characters like \verb|\r|). These issues will be referred to as non-fatal. Fatal formatting issues should cause processing to stop. Non-fatal formatting issues should be automatically corrected according to the most common resolution for this type of error. While downstream processing continues the analyst can double check the automated decision to reformat non-fatal issues. This way workflow would not be slowed for trivial reformatting steps and the more rare problems (e.g. when a missing last new line was caused by incomplete file transfer) could still be caught.   
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Another case to note is when an improperly formatted FASTA file is actually distributed as a component of a bioinformatics tool. Trimmomatic adapter sequences \cite{bolger2014trimmomatic}, for example, are distributed versions of the proprietary Illumina sequencing adapters but the FASTA files are missing final new lines. This can cause issues downstream if a workflow includes common analysis techniques like FASTA file concatenation.   The process of restarting analysis manually after wrapping a FASTA file may only take minutes. The time consuming aspect of this interruption is the time it takes the analyst to become available and the number of jobs this step must be repeated for. Likewise, storage of one extra FASTA file is trivial unless the FASTA file in question stores a whole genome in which case the burden can add up for a bioinformatics core. Efficiency and automation are crucial as bioinformatic analysis projects become more numerous and time consuming. Many tools can either detect a format issue or repair a format issue. No existing tool was found that both validates FASTA format and reformats automatically only where required for a user defined list of non-fatal FASTA format issues.