seq-wrangler

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.

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.

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.

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.

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.

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.