The input data will be considered as paired-end or single-end based on user selection of this option. Also, all selected input files should be single-end OR paired-end only and a mixture of both is not acceptable. ![]() One or multiple FASTQ file(s) (single-end or paired-end) can be selected here. The dialog window has the following further fields/options in the right part: Multiple or even all adapter sequences can be selected at once.įASTQ statistics after Illumina adapter trimming The Illumina adapter sequences for Nextera and TruSeq library prep kits are distributed together with Trimmomatic. In the left part of the dialog the available adapter sequences are listed. When the function is invoked, a dialog windows is opened. Trimmomatic can also be performed manually by using the menu function Tools | Genome Utilities | Illumina Adapter Trimming (Trimmomatic). When performed in the pipeline, Trimmomatic searches for all adapter sequences provided with SeqSphere (see below).Īfter Trimmomatic was performed, the phrase 'adapters trimmed' is added to the procedure details field 'Assembler pre-processing'. It can also be disabled completely or it can be forced to be performed always and independently of FastQC. Therefore, in SeqSphere+ Trimmomatic ( citation) can be used to perform a trimming of Illumina adapter sequences in FASTQ read data.īy default, adapter trimming is automatically performed in a pipeline if adapter sequences were found by FastQC with state 'warning' or 'failed'. ![]() The presence of adapter sequences in next-generation sequencing (NGS) data significantly reduces the quality of assembling and other downstream analysis results. Pipeline script settings for Illumina adapter trimming with Trimmomatic
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