High-speed and accurate color-space short-read alignment with CUSHAW2

TL;DR

This paper introduces an enhanced version of CUSHAW2 that employs a double-seeding strategy to achieve faster and more accurate alignment of color-space short-reads, outperforming existing tools in speed and memory efficiency.

Contribution

The paper presents a novel double-seeding approach in CUSHAW2 that improves sensitivity and speed for color-space short-read alignment, with better performance than SHRiMP2 and BFAST.

Findings

Achieves comparable or better alignment quality than SHRiMP2 and BFAST.

Runs an order of magnitude faster than competing tools.

Uses significantly less peak memory during alignment.

Abstract

Summary: We present an extension of CUSHAW2 for fast and accurate alignments of SOLiD color-space short-reads. Our extension introduces a double-seeding approach to improve mapping sensitivity, by combining maximal exact match seeds and variable-length seeds derived from local alignments. We have compared the performance of CUSHAW2 to SHRiMP2 and BFAST by aligning both simulated and real color-space mate-paired reads to the human genome. The results show that CUSHAW2 achieves comparable or better alignment quality compared to SHRiMP2 and BFAST at an order-of-magnitude faster speed and significantly smaller peak resident memory size. Availability: CUSHAW2 and all simulated datasets are available at http://cushaw2.sourceforge.net. Contact: liuy@uni-mainz.de; bertil.schmidt@uni-mainz.de