CUSHAW statistics

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Associated diseases

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CUSHAW specifications

Information


Unique identifier OMICS_00658
Name CUSHAW
Alternative names CUSHAW2, CUSHAW3, CUSHAW2-GPU, CUSHAW3-UPC
Software type Package/Module, Toolkit/Suite
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C++
Parallelization CUDA
License GNU General Public License version 2.0
Computer skills Advanced
Version 3.0
Stability Stable
Maintained Yes

Versioning


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Documentation


Maintainers


  • person_outline Bertil Schmidt <>
  • person_outline Yongchao Liu <>

Publications for CUSHAW

CUSHAW in publications

 (12)
PMCID: 5846869
PMID: 29568413
DOI: 10.1007/s13258-017-0621-9

[…] with structural variants, bwa–pssm (kerpedjiev et al. ) outperforming the sensitivity of bwa–mem and bowtie 2 using position-specific scoring matrices for high divergent reads such as ancient dna, cushaw3 (liu et al. ) scoring higher sensitivity compared to bwa–mem, bowtie 2 and novoalign for short reads, kart (lin and hsu ) reducing the runtime to about 3–100 times compared to bwa–mem […]

PMCID: 5440850
PMID: 28508884
DOI: 10.1038/ncomms15311

[…] program with default parameters and sequencing base error rates of 1 and 2%. we compare balaur with several popular and efficient state-of-the-art nonprivate read aligners: bwa-mem, bowtie2 (ref. ), cushaw3 (ref. ), alfalfa and soap2 (ref. ). all the experiments were performed on a single 2.67 ghz intel xeon x5550 processor. the accuracy results in a distributed setting will remain the same, […]

PMCID: 5073887
PMID: 27766935
DOI: 10.1186/s12859-016-1216-1

[…] \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$\mathcal {r}$\end{document}r to the reference genome, we considered several popular aligners: bowtie2 [], bwa-sw [], cushaw2 [], smalt [], srmapper [], shrimp2 [], razers [], gassst [], seqalto [], masai [], and soap2 []. most aligners employed a seed-and-extend strategy, which first finds exact matches (seeds) betw […]

PMCID: 5026444
PMID: 27635004
DOI: 10.1128/genomeA.00983-16

[…] j6 was compared to the mtcc234 (ahbe01000000) (), cbs767 (nc_006043.2 to nc_006049.2) (), and cbs789 (lmyn01000000) () genomes. bowtie 2 (), burrows–wheeler alignment (bwa) (), bbmap (), and cushaw2 () were used to align the sequenced reads to the previously mentioned species. qualimap was used to calculate correctly mapped reads to the genomes (). the mapping alignment percentages of j6 […]

PMCID: 4965716
PMID: 27461106
DOI: 10.1186/s40246-016-0068-0

[…] large datasets with low memory footprints by using dsk [], a counting algorithm that requires a user to define a fixed amount of memory and disk space. its error correction process is similar to cushaw [], a procedure also used by musket. in bloocoo, the multi-set of all k-mers present in the reads is partitioned, and partitions are saved to disk. then, each partition is separately loaded […]


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CUSHAW institution(s)
Institut für Informatik, Johannes Gutenberg Universität Mainz, Mainz, Germany
CUSHAW funding source(s)
School of Computational Science & Engineering, Georgia Institute of Technology, Atlanta, GA, USA; Institut für Informatik, Johannes Gutenberg Universität Mainz, Mainz, Germany

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