12 skills · sorted by relevance
Validate FASTQ sequencing files, run local quality checks, and interpret reports to decide whether trimming is needed. Optionally remove adapters or low-quality read ends while preserving original reads and their quality reports.
Use when analyzing FASTQC quality reports from sequencing data, identifying quality issues in NGS datasets, or troubleshooting sequencing problems. Interprets quality metrics and provides actionable recommendations for RNA-seq, DNA-seq, and ChIP-seq data.
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Aggregates QC from 150+ bioinformatics tools into one interactive HTML report. Scans FastQC, samtools, STAR, HISAT2, Trim Galore, featureCounts, Kallisto, Salmon, Picard, GATK logs; merges per-sample stats with plots. For NGS pipeline-wide QC. Use FastQC directly for single-sample; MultiQC for multi-sample reporting.
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Automated sequencing quality control and advanced visualization wrapping FastQC, MultiQC, and custom chart generation. Exposes an MCP stdio server for live AI integration alongside a ClawBio CLI runner.
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Organize ATAC-seq, ChIP-seq, CUT&RUN, or CUT&Tag inputs and route them to suitable analysis workflows. Covers initial quality checks and preparation for finding peaks, genomic regions with concentrated signal, and comparing them across samples.
Check whether a next-generation sequencing workflow has the tools, packages, reference data, and databases it needs. Generate installation and resource setup plans, record available resources, and compare them before rerunning an analysis.
Remove sequencing adapters from FASTQ files using Cutadapt and Trimmomatic. Supports single-end and paired-end reads, Illumina TruSeq, Nextera, and custom adapter sequences. Use when FastQC shows adapter contamination or before alignment of short reads.
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Generate and interpret quality reports from FASTQ files using FastQC and MultiQC. Assess per-base quality, adapter content, GC bias, duplication levels, and overrepresented sequences. Use when performing initial QC on raw sequencing data or validating preprocessing results.
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All-in-one read preprocessing with fastp including adapter trimming, quality filtering, deduplication, base correction, and HTML report generation. Use when preprocessing Illumina data and wanting a single fast tool instead of separate Cutadapt, Trimmomatic, and FastQC steps.
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All-in-one read preprocessing with fastp including adapter trimming, quality filtering, deduplication, base correction, and HTML report generation. Use when preprocessing Illumina data and wanting a single fast tool instead of separate Cutadapt, Trimmomatic, and FastQC steps.
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Generates standardized quality control reports by aggregating metrics from FastQC, alignment, and other tools using MultiQC. Use when summarizing QC metrics across samples, creating shareable quality reports, or building automated QC pipelines.
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Remove sequencing adapters from FASTQ files using Cutadapt and Trimmomatic. Supports single-end and paired-end reads, Illumina TruSeq, Nextera, and custom adapter sequences. Use when FastQC shows adapter contamination or before alignment of short reads.
The English summary is being prepared. Showing the original description.