Adapter and Kmer Sequence Files

To include metrics for adapter or other sequence content, DRAGEN FastQC needs to be provided with the desired sequences in FASTA format. DRAGEN provides two options for this purpose, --fastqc-adapter-file for adapter sequences and --fastqc-kmer-file for any additional kmers of interest so that users can add sequences of interest without changing the expected adapter results.

DRAGEN FastQC can accept up to a combined total of 16 adapters and kmer sequences. Each sequence can be a maximum of 12 bp in length. By default, DRAGEN uses the adapter file located at /opt/edico/config/adapter_sequences.fasta. The file contains the following same adapter sequences as Babraham's FastQC v 0.11.10 and later.

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Illumina Universal Adapter—AGATCGGAAGAG

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Illumina Small RNA 3' Adapter—TGGAATTCTCGG

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Illumina Small RNA 5' Adapter—GATCGTCGGACT

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Nextera Transposase Sequence—CTGTCTCTTATA