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Scientific-ToolingScientific-Tooling/structured-intelligence/skills/genome-read-alignment/SKILL.md

genome-read-alignment

Skill4 starsChanged 12 days agoMITView on GitHub

Align short reads to a reference genome with BWA-MEM2, sort and index with samtools, and mark duplicates with picard.

The file

We split this skill into the rules it gives an agent

3 rules. About 0 are common, 1 is distinctive, and 2 are very specific to this project.

  • ≈0

    Common · estimate

    Many files like this have a rule of this kind.

  • ≈1

    Distinctive · estimate

    This author's own choices. Worth a look.

  • 2

    Very specific

    Tied to their project's names, files or tools. Probably skip.

  • Common
  • Distinctive
  • Very specific
  1. Very specific:

    Read group string (@RG\tID:...\tSM:...\tPL:...\tLB:...\tPU:...).

    line 21
  2. Very specific:

    Run bwa-mem2 mem with the read group, piping output to samtools sort to produce a coordinate-sorted BAM.

    line 32
  3. Distinctive:

    Read group string malformed or missing required fields (ID, SM).

    line 54

≈ “Common” is an estimate: at least 1 in 5 of the 350,495 skill files we read have a rule of the same kind, not the same words. “Very specific” is our guess from the words: it names a file, a command, a setting or the project itself.

Keep what fits and drop the rest. Your version, ready for your agents.
Files
SKILL.md

Skill: genome-read-alignment

Use When

  • User needs to align FASTQ reads to a reference genome.
  • User wants to produce a coordinate-sorted, indexed BAM file.
  • User needs to mark PCR or optical duplicates in aligned reads.
  • User wants to add read group information (@RG) to alignments.

Inputs

  • Required:
    • Trimmed FASTQ file(s) (single-end or paired-end).
    • Reference FASTA, pre-indexed for BWA-MEM2.
  • Optional:
    • Read group string (@RG\tID:...\tSM:...\tPL:...\tLB:...\tPU:...).
    • Number of threads (default: 4).
    • Output directory (default: current directory).
    • Temporary directory for sorting/dedup intermediates.
    • Optical duplicate pixel distance (default: 2500 for patterned flowcells).
    • Mark-duplicate tool choice: picard (default) or samtools markdup.

Workflow

  1. Validate that reference index files exist (.0123, .amb, .ann, .bwt.2bit.64, .pac, .fai, .dict).
  2. Construct a read group string from sample metadata if one is not provided (fields: ID, SM, PL, LB, PU).
  3. Run bwa-mem2 mem with the read group, piping output to samtools sort to produce a coordinate-sorted BAM.
  4. Index the sorted BAM with samtools index.
  5. Mark duplicates with picard MarkDuplicates (or samtools markdup if selected).
  6. Index the deduplicated BAM.
  7. Report alignment summary: total reads, mapped reads, properly paired reads, duplicate reads, mapping rate.

Output Contract

  • Coordinate-sorted deduplicated BAM file (.bam).
  • BAM index file (.bai).
  • Duplicate metrics file (picard MarkDuplicates output).
  • Alignment summary statistics (total, mapped, properly paired, duplicates, mapping rate).

Limits

  • BWA-MEM2, samtools, and picard must be installed and available on $PATH.
  • The BWA-MEM2 index must be pre-built (bwa-mem2 index <ref.fa>).
  • Memory scales with reference genome size (~8 GB for human GRCh38).
  • Picard requires a Java runtime (Java 8+).
  • This skill handles single-sample alignment only; multi-sample merging is out of scope.
  • Common failure cases:
    • Reference index files missing or incomplete (e.g., .bwt.2bit.64 absent).
    • Read group string malformed or missing required fields (ID, SM).
    • Insufficient memory for BWA-MEM2 index loading (~8 GB for human genome).

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