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Sequence QC, alignment, and BAM processing. Wraps FastQC, BWA/Bowtie2, SAMtools for automated read-to-BAM pipelines.
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Based on SOC occupation classification
Convert raw Nanopore signal data (FAST5/POD5) to nucleotide sequences using Dorado basecaller. Covers model selection, GPU acceleration, modified base detection, and quality filtering. Use when processing raw Nanopore data before alignment. Note: Guppy is deprecated; use Dorado for all new analyses.
Meta-agent that routes bioinformatics requests to specialised sub-skills. Handles file type detection, analysis planning, report generation, and reproducibility export.
Ancestry decomposition PCA against the Simons Genome Diversity Project
Shotgun metagenomics profiling — taxonomy, resistome, and functional pathways
Semantic Similarity Index for disease research literature using PubMedBERT embeddings
Query the ClinPGx API for pharmacogenomic gene-drug data, clinical annotations, CPIC guidelines, and FDA drug labels
| name | seq-wrangler |
| description | Sequence QC, alignment, and BAM processing. Wraps FastQC, BWA/Bowtie2, SAMtools for automated read-to-BAM pipelines. |
| version | 0.1.0 |
| metadata | {"genetind":{"requires":{"bins":["python3","samtools"],"anyBins":["bwa","bowtie2","minimap2"],"env":[],"config":[]},"always":false,"emoji":"🦖","homepage":"https://github.com/ClawBio/ClawBio","os":["macos","linux"],"install":[{"kind":"brew","formula":"samtools","bins":["samtools"]},{"kind":"brew","formula":"bwa","bins":["bwa"]}]}} |
You are the Seq Wrangler, a specialised agent for sequence data QC, alignment, and processing.
samtools (BAM manipulation)bwa or bowtie2 or minimap2 (alignment)fastqc, fastp, multiqc, picardPlanned -- implementation targeting Week 4-5 (Mar 20 - Apr 2).