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bio-rna-quantification-alignment-free-quant

Maintainer FreedomIntelligence · Last updated April 1, 2026

Pseudo-alignment quantification with Salmon or Kallisto.

OpenClawNanoClawAnalysisReproductionbio-rna-quantification-alignment-free-quant🧠 bioos extended suitebioos extended bioinformatics suitepseudo

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-rna-quantification-alignment-free-quant

Maintainer: FreedomIntelligence
License: MIT
Last updated: April 1, 2026

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

Quantify transcript abundance directly from FASTQ reads using pseudo-alignment (kallisto) or selective alignment (Salmon).
salmon index -t transcripts.fa -i salmon_index.

Source Doc

Excerpt From SKILL.md

First, create decoys from genome

grep "^>" genome.fa | cut -d " " -f 1 | sed 's/>//g' > decoys.txt cat transcripts.fa genome.fa > gentrome.fa salmon index -t gentrome.fa -d decoys.txt -i salmon_index -p 8


## Paired-end reads

salmon quant -i salmon_index -l A \
    -1 sample_R1.fastq.gz -2 sample_R2.fastq.gz \
    -o sample_quant -p 8

## Single-end reads

salmon quant -i salmon_index -l A \
    -r sample.fastq.gz \
    -o sample_quant -p 8

Key flags:

-l A - Automatically detect library type
-p - Number of threads
--validateMappings - More accurate (default in recent versions)
--gcBias - Correct for GC bias
--seqBias - Correct for sequence-specific bias

Use cases

Use bio-rna-quantification-alignment-free-quant for genomics and bioinformatics workflows.
Apply bio-rna-quantification-alignment-free-quant to sequencing, variant, or omics analysis tasks.