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umi-processing

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Extracts UMIs and collapses reads to original molecules with umi_tools (directional dedup) or builds error-corrected single-strand/duplex consensus reads with fgbio. Use when the library has UMIs and accurate molecule counting or below-sequencer-floor error correction is needed - single-cell, low-input RNA-seq, targeted panels, and ctDNA/liquid-biopsy rare-variant detection. For UMI extraction during QC use fastp-workflow; do not dedup non-UMI bulk RNA-seq.

When to use

• UMI extraction
• directional dedup
• molecule counting
• single-strand consensus reads
• duplex consensus reads
• single-cell RNA-seq
• low-input RNA-seq
• ctDNA/liquid-biopsy rare-variant detection

When not to use

• UMI extraction during QC
• non-UMI bulk RNA-seq deduplication
• single-cell matrix preprocessing
• non-UMI DNA coordinate dedup

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