seq-wrangler

What problem does it solve?

Seq Wrangler automates the repetitive, multi-step tasks required to turn raw sequencing reads into analysis-ready BAM files, eliminating manual orchestration of QC, trimming, alignment, and BAM processing across samples.

Core Features & Use Cases

• Read QC and aggregation: Run FastQC and produce MultiQC summaries to identify quality issues across libraries.
• Adapter trimming and preprocessing: Integrate fastp or Trimmomatic for adapter removal and basic read filtering.
• Alignment and BAM processing: Align with BWA/Bowtie2/Minimap2, then sort, index, mark duplicates, and compute coverage with samtools and related tools.
• Pipeline export: Generate reproducible shell scripts or Nextflow pipelines and export environment specifications and checksums for reproducibility.
• Use Case: Process paired-end Illumina samples to produce deduplicated, sorted, and indexed BAMs with aggregated QC reports for downstream variant calling or coverage analysis.

Quick Start

Run QC on sample_R1.fastq/sample_R2.fastq, trim adapters, align to GRCh38, and produce a sorted, indexed BAM plus a MultiQC report.