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EULER-SR specifications

Information


Unique identifier OMICS_00015
Name EULER-SR
Software type Package/Module
Interface Command line interface, Application programming interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Maintained No

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This tool is not maintained anymore.

Publications for EULER-SR

EULER-SR citations

 (24)
library_books

Assessment of Epstein Barr virus nucleic acids in gastric but not in breast cancer by next generation sequencing of pooled Mexican samples

2016
PMCID: 4804503
PMID: 26910355
DOI: 10.1590/0074-02760150405

[…] initial sequences of the samples have a length of 36-mer. those reads obtained for all samples (in fastq format) were filtered from undesired sequences using the assembly perl tools from the euler-sr program (). then, a collection of programs developed with the lazarus free pascal programming language was used to (i) eliminate sequences of low complexity such as mononucleotide repeats, […]

library_books

Identification and Assessment of the Potential Allergenicity of 7S Vicilins in Olive (Olea europaea L.) Seeds

2016
PMCID: 4789380
PMID: 27034939
DOI: 10.1155/2016/4946872

[…] of different algorithms to correct bias and to produce the best available assembly. to generate primary contigs, mira3 (based on overlap-layout-consensus-based algorithms) and de brujin graph-based euler-sr software was used. contigs were further exposed to consensus using cap3 software. such strategy was similar to that designed to generate a reproductive transcriptome in olive []. preliminary […]

library_books

Genomes and virulence difference between two physiological races of Phytophthora nicotianae

2016
PMCID: 4730604
PMID: 26823972
DOI: 10.1186/s13742-016-0108-7

[…] hybrid assembly approach to assemble the genome of race 0 (fig. ). we also compared the performance of different assemblers including velvet (v1.2.09) [], abyss (v3.81) [], jr-assembler (v1.0.3) [], euler-sr (v1.1.2) [], spades (v3.0.0) [], soapdenovo2 (r240) [], celera assembler (v8.0) [] and minimus2 (v 3.1) [] on p. nicotianae race 0. comparison showed that assemblies from pacbio reads […]

library_books

Is the whole greater than the sum of its parts? De novo assembly strategies for bacterial genomes based on paired end sequencing

2015
PMCID: 4552406
PMID: 26315384
DOI: 10.1186/s12864-015-1859-8

[…] algorithms or strategies for de novo assembly. many de novo assemblers utilizing the de bruijn graph-based approach were developed for ngs reads, such as velvet, soapdenovo, allpaths, edena, euler-sr, and euler-usr [–]. these methods construct de bruijn graphs from short reads and obtain contigs by solving the graphs. other studies come from a theoretical perspective and discuss whether […]

library_books

Denoising DNA deep sequencing data—high throughput sequencing errors and their correction

2015
PMCID: 4719071
PMID: 26026159
DOI: 10.1093/bib/bbv029

[…] chosen manually from experience—e.g. in euler [, ] and soapdenovo [, ]—more objective criteria to derive the threshold from the actual data were soon developed (, supplementary table s2)., in euler-sr, the threshold was chosen manually, but an explicit reasoning for the choice was provided []: given the number of reads (n), their average length (l), an approximate genome size (g) […]

library_books

A Roadmap for Natural Product Discovery Based on Large Scale Genomics and Metabolomics

2014
PMCID: 4201863
PMID: 25262415
DOI: 10.1038/nchembio.1659

[…] on an illumina hiseq using v2 chemistry at the university of illinois. for these 87 genomes, an initial set of genome assemblies was performed using velvet version 1.0.15 , soapdenovo v1.04 , euler-sr v1.1.2 . subsequently, faux reads created by breaking larger contigs from these assemblies into 1999 bp pieces and 400,000 reformatted illumina paired-end reads were used as input […]


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EULER-SR institution(s)
Bioinformatics Program, University of California San Diego, La Jolla, CA, USA; Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
EULER-SR funding source(s)
This research was supported by NIH grant 1R21HG004130-01 and by NSF Infrastructure grant EIA-0303622.

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