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bwa

Fast and accurate DNA sequence alignment using Burrow-Wheeler Transform

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About

Burrow-Wheeler Aligner for pairwise alignment of DNA

Commands

bwa

Examples

Index a reference genome FASTA file for alignment$ bwa index reference.fa
Align paired-end reads to reference genome and output SAM file$ bwa mem reference.fa reads_R1.fastq reads_R2.fastq > alignment.sam
Align single-end reads with custom parameters$ bwa mem -t 8 reference.fa reads.fastq | samtools view -b -o output.bam