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ksahlin authored Apr 17, 2022
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strobealign
==============

Strobealign is a fast short-read aligner. It achieves the speedup by using a dynamic seed size obtained from syncmer-thinned strobemers. Strobealign is multithreaded, implements alignment (SAM) and mapping (PAF), and benchmarked for SE and PE reads of lengths between 100-300bp. A preprint describing **v0.4** is available [here](https://doi.org/10.1101/2021.06.18.449070). **Current version is 0.7**.
Strobealign is a fast short-read aligner. It achieves the speedup by using a dynamic seed size obtained from syncmer-thinned strobemers. Strobealign is multithreaded, implements alignment (SAM) and mapping (PAF), and benchmarked for SE and PE reads of lengths between 100-300bp. A preprint describing **v0.4** is available [here](https://doi.org/10.1101/2021.06.18.449070). **Current version is 0.7.1**.

See [INSTALLATION](https://github.com/ksahlin/StrobeAlign#installation) and [USAGE](https://github.com/ksahlin/StrobeAlign#usage) to install and run strobealign. See [v07 PERFORMANCE](https://github.com/ksahlin/StrobeAlign#v07-performance) for the updated accuracy and runtime performance of strobealign and [release notes](https://github.com/ksahlin/StrobeAlign/releases) for all the updates since v0.4 described in the preprint.

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