Trimmomatic is a popular tool for trimming adapter sequences from Illumina reads. If you wish to use any of these applications, both FASTQ and FASTA files are available for that purpose. Adapter trimming software applications may require FASTQ or FASTA formatted files. Our bioinformatics data analysis pipelines automatically convert FASTQ files to FASTA files, so you will receive both file formats at the end of each sequencing run. They represent the raw data files from which all downstream processing begins. FASTQ files are automatically generated by Illumina sequencers. We deliver sequencing results in FASTQ and FASTA file formats. The adapter sequences for other kits may be different, so be sure to check which kit was used for library prep and get the appropriate sequence from the adapter sequences manual. Illumina Nextera XT is one of our most used kits. The exact DNA sequence of the adapters depends on the library preparation kit that is used for sequencing. This step will improve downstream data processing, such as sequence alignments and de novo assembly. When sequencing is complete it’s important to remove or trim off, the adapter sequences from the reads.
The adapter sequences are required for attaching reads to flow cells and for attaching indexes to reads. During the library preparation process, Illumina adapter sequences are annealed to sequencing reads.
