This repository streamlines the conversion of raw DNA sequencing data from FASTQ to BAM format, incorporating scripts that not only facilitate BAM conversion but also generate Sequence Alignment Map (SAM) files.
Utilizing Minimap2 and Samtools for efficient data processing and analysis."
Align FASTQ to reference genome using minimap2 Convert SAM to BAM using samtools Replace ref_genome.fa, SRR26624132_1.fastq, and SRR26624132_2.fastq with your actual files.
brew install samtools
brew install minimap2
minimap2 -t 8 -a -x sr ref_genome.fa SRR26624132_1.fastq SRR26624132_2.fastq -o out_sam.sam
samtools view -bS out_sam.sam > final.bam