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bio-read-alignment-bowtie2-alignment

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Align short reads using Bowtie2 with local or end-to-end modes. Supports gapped alignment for ChIP-seq, ATAC-seq, or when flexible alignment modes are needed.

When to use

• Aligning ChIP-seq
• Aligning ATAC-seq
• Flexible alignment modes
• Gapped alignment
• Paired-end read alignment
• Single-end read alignment
• Building Bowtie2 index

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