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alignment-free-quant

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Quantify transcript expression from FASTQ with Salmon (selective alignment) or kallisto (pseudoalignment), bypassing genome mapping. Use when quantifying RNA-seq without alignment, deciding whether a decoy-aware index is required, detecting and verifying library strandedness, enabling GC and sequence bias correction, or choosing whether to generate inferential replicates (bootstraps/Gibbs) for transcript-level downstream testing.

When to use

• Quantifying RNA-seq without alignment
• Deciding whether a decoy-aware index is required
• Detecting and verifying library strandedness
• Enabling GC and sequence bias correction
• Choosing whether to generate inferential replicates
• Transcript-level downstream testing

When not to use

• Gene-level DESeq2/edgeR via tximport

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