bio-rna-quantification-alignment-free-quant
Quantify transcript expression using pseudo-alignment with Salmon or kallisto. Use when quantifying transcripts with Salmon or kallisto.
npx skills add BioTender-max/awesome-bio-agent-skills --skill alignment-free-quant --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
## Version Compatibility Reference examples tested with: Salmon 1.10+, fastp 0.23+, kallisto 0.50+, pandas 2.2+ Before using code patterns, verify installed versions match. If versions differ: - CLI: `<tool> --version` then `<tool> --help` to confirm flags If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # Alignment-Free Quantification **"Quantify gene expression without alignment"** → Estimate transcript abundances directly from FASTQ reads using pseudo-alignment or selective alignment, bypassing genome mapping. - CLI: `salmon quant -i index -l A -1 R1.fq.gz -2 R2.fq.gz -o quant/`, `kallisto quant -i index -o output R1.fq.gz R2.fq.gz` Quantify transcript abundance directly from FASTQ reads using pseudo-alignment (kallisto) or selective alignment (Salmon). ## Salmon Workflow ### Build Index ```bash # Download transcriptome FASTA # Ensembl: Homo_sapiens.GRCh38.cdna.all.fa.gz # Basic index (fast, less accurate) salmon index -t transcripts.fa -i salmon_index # Decoy-aware index (recommended for accuracy) # First, create decoys from genome grep "^>" genome.fa | cut -d " " -f 1
- Version Compatibility
- Salmon Workflow
- Build Index
- Quantify Samples
- Library Types
- Batch Processing
- Output Files
- kallisto Workflow
- Salmon vs kallisto
- Combining Results
- Quality Checks
- Common Issues
- Related Skills
Download transcriptome FASTA Basic index (fast, less accurate) salmon index -t transcripts.fa -i salmon_index Decoy-aware index (recommended for accuracy) 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 \ Single-end reads
What does the bio-rna-quantification-alignment-free-quant skill do?
Quantify transcript expression using pseudo-alignment with Salmon or kallisto. Use when quantifying transcripts with Salmon or kallisto.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill alignment-free-quant --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.