The application uses two approaches to detect technical sequences within the reads: Simple mode: The simple mode approach works by finding an approximate match between the read and supplied technical sequences. Please, cite Trimmomatic as Bolger AM, Lohse M, Usadel B (2014).Īdapter Removal This step is used to find and remove adapters and contaminant sequences. Trimmomatic is a fast, multithreaded command line tool that can be used to trim and crop sequencing data as well as to remove adapters. The FASTQ Preprocessing tool uses the well-known preprocessing software Trimmomatic. In this way, problems and biases can be detected, which allows to better configure the preprocessing procedure. These problems eventually lead to erroneous conclusions in processes such as assembly and alignment, so a preprocessing step is necessary to produce better analysis results.īefore proceeding, it is advisable to carry out a quality control check of the sequencing data within OmicsBox (FASTQ Quality Check).
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