This is the Linux app named CUSHAW3: Accurate Short-read Alignment whose latest release can be downloaded as cushaw3-v3.0.3.tar.bz2. It can be run online in the free hosting provider OnWorks for workstations.
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CUSHAW3: Accurate Short-read Alignment
CUSHAW3 is an open-source parallelized, sensitive and accurate short-read aligner. This aligner proposes a general approach to properly aligning both easy and hard reads to large genomes such as the human genome. Perform evaluation on alignment quality reals that CUSHAW3 consistently outperforms CUSHAW2, BWA-MEM, Bowtie2 and GEM in terms of single-end and paired-end alignment. Furthermore, our aligner has demonstrated better paired-end alignment performance than Novalign3 for short-reads with high error rates.
This is an application that can also be fetched from https://sourceforge.net/projects/cushaw3/. It has been hosted in OnWorks in order to be run online in an easiest way from one of our free Operative Systems.