Genomic Sequence Batch Alignment and Quality Control

Create a comprehensive Bash workflow for processing next-generation sequencing (NGS) FASTQ files that: 1) Performs quality trimming using cutadapt, 2) Runs multi-threaded alignment against reference genome using BWA-MEM, 3) Generates comprehensive quality metrics with FastQC, 4) Automatically detects and flags potential sequencing artifacts, 5) Generates a consolidated HTML report summarizing alignment statistics, 6) Implements configurable thresholds for read quality and coverage.