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Protocols

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

Versioning


No version available

Maintainer


This tool is not maintained anymore.

Publications for EULER-SR

EULER-SR citations

 (12)
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

[…] esulting 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, (i […]

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

[…] sticated 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 t […]

call_split

SeedsGraph: an efficient assembler for next generation sequencing data

2015
BMC Med Genomics
PMCID: 4460749
PMID: 26044652
DOI: 10.1186/1755-8794-8-S2-S13
call_split See protocol

[…] a path. The graph itself does not store individual reads or their overlaps, and compresses redundant sequences. There are also many typical de Bruijn graph-based software programs, such as Velvet [], EULER-SR [], Abyss [], and so forth. However, reducing short reads into even shorter units compromises the ability of disambiguation of short repeats. Another disadvantage is the loss of long-range co […]

library_books

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

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

[…] quenced 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 for gsAssem […]

library_books

Next Generation Sequence Assembly: Four Stages of Data Processing and Computational Challenges

2013
PLoS Comput Biol
PMCID: 3861042
PMID: 24348224
DOI: 10.1371/journal.pcbi.1003345

[…] are filled with N characters that denote unknown bases between them and the total number of N can be estimated easily using paired-end constraints . Some assemblers include scaffolding modules (e.g., Euler-SR, ALLPATHS-LG, Velvet, SGA, SOAPdenovo, and Shorty) (see ) while others are stand-alone scaffolders such as Bambus , , SSPACE , SOPRA , MIP scaffolder , Opera , and SCARPA (see ).There are ma […]

library_books

Development of 32 EST SSR markers for Abies firma (Pinaceae) and their transferability to related species1

2013
Appl Plant Sci
PMCID: 4105371
PMID: 25202517
DOI: 10.3732/apps.1200464

[…] erred to as unigenes). Using the resultant unigene library, PCR amplicon primers were designed using MISA () and Primer3 (), after trimming low quality regions using the qualityTrimmer command in the Euler-SR package (). The criteria applied to identify microsatellite loci were at least six dinucleotide repeat units, or five tri- to hexanucleotide repeat units. To eliminate redundancy (i.e., multi […]

Citations

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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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