CUSHAW3

CUSHAW3 is a software tool that aligns short-read sequences to large genomes with high accuracy and sensitivity. It is an open-source, parallelized aligner with a hybrid seeding approach with three different seed types: maximal exact-match seeds, exact-match k-mer seeds, and variable-length seeds. Additionally, it incorporates techniques such as weighted seed-pairing heuristic, paired-end alignment pair ranking, and read mate rescuing to facilitate accurate paired-end alignment.

CUSHAW3 outperforms other base-space and color-space aligners like Novoalign, CUSHAW2, BWA-MEM, Bowtie2, GEM, SHRiMP2, and BFAST, particularly in terms of single-end and paired-end alignment. The aligner has been extensively tested on simulated and real reads and consistently performs better than its competitors.

CUSHAW3 has been compared to other aligners for base-space alignment by aligning both simulated and real reads to the human genome. The results show that CUSHAW3 consistently outperforms CUSHAW2, BWA-MEM, Bowtie2, and GEM regarding single-end and paired-end alignment. Furthermore, CUSHAW3 has demonstrated better paired-end alignment performance than Novoalign for short reads with high error rates.

CUSHAW3 is consistently one of the best aligners for color-space alignment compared to SHRiMP2 and BFAST. This aligner has demonstrated its ability to accurately align short-read sequences to large genomes, which is a critical task in bioinformatics research.

Topic

Sequencing;Nucleic acid structure analysis;Genomics;Whole genome sequencing

Detail

  • Operation: Sequence alignment

  • Software interface: Command-line user interface

  • Language: C, C++

  • License: -

  • Cost: Free

  • Version name: 3.0.3

  • Credit: -

  • Input: -

  • Output: -

  • Contact: Dr. Yongchao Liu yongchao.ly@alibaba-inc.com

  • Collection: -

  • Maturity: Stable

Publications

  • CUSHAW3: sensitive and accurate base-space and color-space short-read alignment with hybrid seeding.
  • Liu Y, et al. CUSHAW3: sensitive and accurate base-space and color-space short-read alignment with hybrid seeding. CUSHAW3: sensitive and accurate base-space and color-space short-read alignment with hybrid seeding. 2014; 9:e86869. doi: 10.1371/journal.pone.0086869
  • https://doi.org/10.1371/journal.pone.0086869
  • PMID: 24466273
  • PMC: PMC3899341
  • Parallel and Scalable Short-Read Alignment on Multi-Core Clusters Using UPC+.
  • González-Domínguez J, et al. Parallel and Scalable Short-Read Alignment on Multi-Core Clusters Using UPC+. Parallel and Scalable Short-Read Alignment on Multi-Core Clusters Using UPC+. 2016; 11:e0145490. doi: 10.1371/journal.pone.0145490
  • https://doi.org/10.1371/journal.pone.0145490
  • PMID: 26731399
  • PMC: PMC4711716

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