E-MEM specifications

Information


Unique identifier OMICS_08451
Name E-MEM
Alternative name Efficient computation of Maximal Exact Matches
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C++
Parallelization OpenMP
Computer skills Advanced
Stability Stable
Maintained Yes

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Versioning


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Maintainer


  • person_outline Lucian Ilie

Publication for Efficient computation of Maximal Exact Matches

E-MEM citations

 (2)
library_books

LASER: Large genome ASsembly EvaluatoR

2015
BMC Res Notes
PMCID: 4657217
PMID: 26601933
DOI: 10.1186/s13104-015-1682-y

[…] The most time consuming stage of QUAST is, by far, the maximal exact match (MEM) computation step of the alignment process, performed using the NUCmer aligner from MUMmer v3.23 []. Our recent E-MEM tool [] clearly outperforms not only MUMmer but also the currently best tools for MEM computation in large genomes: [–]. It was therefore a natural choice for replacing MUMmer.Besides using E-ME […]

library_books

Alignment of Short Reads: A Crucial Step for Application of Next Generation Sequencing Data in Precision Medicine

2015
PMCID: 4695832
PMID: 26610555
DOI: 10.3390/pharmaceutics7040523

[…] uses a new index structure called longest common prefix (LCP) array and the backward search method of the FM-index and achieves a good tradeoff between mapping speed and memory usage. More recently, E-MEM was developed by Nilesh to decipher MEMs in large genome sequences. E-MEM uses much less memory and is highly amenable to parallelization. It has been reported that all MEMs of minimum length 10 […]

E-MEM institution(s)
Department of Computer Science, University of Western Ontario, London, ON, Canada
E-MEM funding source(s)
This work was supported by the Natural Sciences and Engineering Research Council of Canada (NSERC) Discovery Grant R3143A01.

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