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adapter-trimming

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Removes sequencing adapters from FASTQ reads with Cutadapt and Trimmomatic, including paired-end read-through, small-RNA 3' adapters, amplicon primers, and anchored/linked adapters. Use when FastQC shows adapter content climbing toward the 3' end, when inserts are shorter than the read length (small-RNA, cfDNA, FFPE), or before assembly/k-mer analysis. For all-in-one trimming use fastp-workflow; for quality/length filtering use quality-filtering.

When to use

• removing 3' adapter introduced by read-through
• small-RNA 3' adapter removal
• amplicon/16S primer removal
• anchored/linked adapter removal
• paired-end read-through detection
• length-filtering survivors after trimming

When not to use

• all-in-one trimming workflows
• quality/length filtering as standalone goals
• contaminant/PhiX k-mer removal
• quality-score trimming for alignment-based DNA/RNA

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