bwa-mem2-dna-aligner

What problem does it solve?

This Skill efficiently aligns short DNA sequencing reads to a reference genome, a crucial first step for variant calling and genomic analysis.

Core Features & Use Cases

• High-throughput Alignment: Processes whole-genome, whole-exome, and ChIP-seq data rapidly.
• GATK Compatibility: Generates SAM/BAM files with required read group headers for downstream analysis with GATK.
• Use Case: Align millions of DNA sequencing reads from a patient's exome data to the human reference genome to prepare for identifying genetic mutations.

Quick Start

Align paired-end DNA reads from sample1_R1.fastq.gz and sample1_R2.fastq.gz to the GRCh38 reference genome.