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quality-filtering

separate

Filters reads by quality, length, N content, and complexity with Trimmomatic, fastp, and Cutadapt, including sliding-window trimming, per-read unqualified-base filtering, and 2-color poly-G removal. Use when reads have poor-quality tails, when an assembly or k-mer workflow needs clean input, or when a junk read subpopulation must be dropped. For adapter removal use adapter-trimming; for all-in-one preprocessing use fastp-workflow.

When to use

• Filter reads by quality
• Sliding-window trimming
• Per-read unqualified-base filtering
• 2-color poly-G removal
• Remove low-quality bases
• Discard reads below quality/length thresholds
• Drop junk read subpopulation
• Clean input for assembly or k-mer workflow

When not to use

• Adapter removal
• All-in-one preprocessing
• Contamination removal
• Reading quality plots

Skill page

Source