seq-wrangler

Automate NGS read alignment and processing from FASTQ to BAM.

Updated May 10, 2026

Search Tags:#quality control #data processing #alignment #bam #ngs

Ready to run

npx skills add https://github.com/MubasherMohammed/opencode-BioInfo --skill seq-wrangler-mubashermohammed

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: seq-wrangler
Source: https://github.com/MubasherMohammed/opencode-BioInfo/tree/main/python/skills/seq-wrangler
Command: npx skills add https://github.com/MubasherMohammed/opencode-BioInfo --skill seq-wrangler-mubashermohammed

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires samtools, bwa, bowtie2, minimap2, fastqc, fastp, multiqc, and includes scripts (resource) and references (resource) and assets (resource) components.

What problem does it solve?

Seq Wrangler addresses the complexity and tedium of NGS data analysis by automating the entire process, from read QC and alignment to BAM processing and statistical analysis.

Core Features & Use Cases

NGS Read QC: Ensures the quality of NGS data through FastQC, adapter trimming, and alignment filtering.
Alignment: Integrates BWA/Bowtie2/Minimap2 for robust read alignment to reference genomes.
BAM Processing: Offers a suite of tools for BAM processing, including sorting, marking duplicates, and indexing.
Use Case: With this Skill, you can align reads to a reference genome, generate QC reports, and perform comprehensive analysis on your NGS data.

Quick Start

Use the seq-wrangler skill to align reads and process your NGS data. Run: 'seq-wrangler align mydata.R1.fastq.gz mydata.R2.fastq.gz -i /ref/hg38 -o output_dir/'

Frequently Asked Questions about seq-wrangler

High-intent search queries and answers about installing and using this skill.

FAQPage Schema

How do I automate NGS read alignment and BAM processing from fastq files?▼

To automate NGS read alignment and BAM processing, use a pipeline that integrates BWA, Bowtie2, Minimap2, and SAMtools to streamline the workflow from fastq files to final BAM outputs, including sorting, marking duplicates, and indexing.

What is the best way to run FastQC and adapter trimming before read alignment?▼

Run FastQC and adapter trimming using an automated NGS pipeline that executes FastQC for quality control and Fastp for adapter trimming, ensuring high-quality reads before proceeding to alignment with BWA, Bowtie2, or Minimap2.

Do I need samtools and bwa installed to process NGS data with this pipeline?▼

Yes, you must install samtools, bwa, bowtie2, minimap2, fastqc, fastp, and multiqc to process NGS data. These dependencies are required to execute the alignment, quality control, and BAM processing steps.

Can I generate a multiqc report automatically after read alignment and QC?▼

Yes, you can generate a multiqc report automatically. The pipeline offers optional multiqc report generation to summarize FastQC, Fastp, and alignment filtering results into a comprehensive quality control report.

How do I align paired-end fastq reads to a reference genome using bwa or bowtie2?▼

Align paired-end fastq reads to a reference genome using bwa or bowtie2 by passing R1 and R2 fastq files and a reference index to the pipeline, which automates the alignment and subsequent BAM sorting and indexing into a specified output directory.

When should I use minimap2 instead of bwa for NGS read alignment?▼

The pipeline integrates BWA, Bowtie2, and Minimap2 to provide robust read alignment to reference genomes, allowing you to select the appropriate aligner for your specific NGS data type and reference genome.