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# Description
Precise Assessment of Indels in Rust (PAIRS) is a tool for detecting insertion/deletion/substituion (indels) events in DNA sequences following CRISPR treatments. It operates on short read, deep sequence data. It is designed to be fast while maintaining a high degree of accuracy. To achieve this, it uses a hybrid combination of a custom implementation of the Prefixed Index Counting (PIC) algorithm introduced by [Lee et al., 2020](https://doi.org/10.1093/nargab/lqaa012) and the Block Aligner introduced by [Liu and Steinegger, 2023](https://doi.org/10.1093/bioinformatics/btad487).

# Installation
Not there yet. To test at this stage, install rustup, clone the repository and run `make compile/debug`.