# Aligning sequence from molecular inversion probes

## TL;DR

This paper introduces bwa-mips, a software tool for aligning genomic sequences from molecular inversion probes.

## Contribution

The novel contribution is a unified program for mapping, arm removal, and deduplication of MIP sequences.

## Key findings

- bwa-mips simplifies the alignment process for molecular inversion probe data.
- The tool outputs alignments in SAM format after processing.
- It is available as open-source software under the MIT license.

## Abstract

Molecular inversion probes (MIP’s) allow efficient enrichment of genomic regions of interest for the purpose of targeted sequencing. To date, there is a paucity of simple-to-use software to align sequences derived from this method. Here, we describe a single program that performs mapping, arm removal, and deduplication before outputting alignments in SAM format.

bwa-mips is available at https://github.com/brentp/bwa-mips under the MIT license.

bpederse@gmail.com