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Sequence quality control and alignment v1.0.0
Use this resource to process sequencing data, from quality control to BAM file
New
- 568 downloads
- 119 likes
- 147 saves
Free
Install with the CLI
In a terminal, from the folder you want:
npx --yes palatekit@latest install sequencing-qc-alignment-pipelineWith no option, the skill goes to ~/.agents/skills/; add --agent claude-code (or codex, cursor…) to target an agent.
First time: connect the CLI with
npx --yes palatekit@latest loginThe agent runs FastQC, trims adapters with fastp or Trimmomatic, aligns reads with BWA-MEM2, Bowtie2 or Minimap2, then sorts, indexes and computes coverage. You get a MultiQC report and a reproducible pipeline.
Mostly picked by
Updated November 2, 2026
Previews
Details
- Install guides
- Generates with
- Your agent's model
- Licence
- MIT
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What you get
- SKILL.md: quality control, adapter trimming and alignment
- SKILL.md: BAM processing, MultiQC report and export of the workflow as a shell script or Nextflow pipeline
Good fit for
- You receive sequencing reads that must be checked before analysis
- You want to turn a series of steps into a reproducible pipeline
Not for
Tags
- sequencing
- alignment
- bam
- quality control
About
You say
“Check the quality of these reads, trim the adapters, then align them to the reference genome.”
Skill published by aaaaqwq under the MIT license, delivered in its original version.
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How to use it
- Install the skill in your agent's skills folder
- Ask your agent to process sequencing data, from quality control to BAM file
- Review and adjust the result
Content preview
Files
- LICENSE1.1 KB
- NOTICE-PALATEKIT.md0.5 KB
- SKILL.md1.7 KB
Origin and licence
Listed unmodified
- Author
- aaaaqwq
- Source
- github.com/aaaaqwq/agi-super-team/tree/4c7b20bc52ad8d4a89fa3f5185abc455ef9248de/skills/seq-wrangler
- Licence
- MIT
Notice
« seq-wrangler » (aaaaqwq, MIT) livré dans sa version d'origine : fiche en français et en anglais par PalateKit.
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