What it does

Seq Wrangler is a domain-specific skill that equips an agent to perform sequence data quality control, adapter trimming, alignment to reference genomes, BAM processing (sort, index, mark duplicates), coverage stats, and MultiQC aggregation. It also helps export full pipelines as shell scripts or Nextflow workflows.

When to use it

Use this skill when processing NGS FASTQ data: running FastQC, trimming adapters, aligning reads with BWA/Bowtie2/Minimap2, and producing analysis-ready BAMs with SAMtools/picard. It's intended for bioinformatics pipelines and labs that need reproducible, automated sequence-processing steps.

What's included

Scripts: examples and commands for FastQC, fastp/Trimmomatic, alignment with BWA/Bowtie2/Minimap2, and SAMtools-based BAM processing (described in skill body).
References: dependency notes and install hints for samtools, aligners, and optional tools like multiqc and picard.
Instructions: example queries and step-by-step workflows for QC, trimming, alignment, coverage calculation, and pipeline export.