Introduction

This is the github page for a chimeric alignment engine rearr. Although rearr can be used for any chimeric alignment job in theory, rearr is mainly used to analyze CRISPR editing data.

The CRISPR editing output is highly chimeric due to the following reasons.

• Interplay of stagger cleavage, MMEJ and unilateral.
• Random insertion with or without template.
• Unlisted/Unknown machanisms.

Most current tools rely on non-chimeric alignment engines. rearr implements a chimeric alignment engine by applying the Smith-Waterman algorithm twice.

rearr is very efficient in both time and space.

• rearr generalizes Farrar’s SIMD to the chimeric alignment.
• rearr implements a novel branch-and-bound backtrack process to get the optimal alignment in linear space. This method is more efficient in time compared with the famous linear-space implementation based on divide and conquer.

Accessibility

See the project README.md rearr.