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Edena specifications

Information


Unique identifier OMICS_00014
Name Edena
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline David Hernandez

Publication for Edena

Edena citations

 (81)
library_books

Genome comparison of different Zymomonas mobilis strains provides insights on conservation of the evolution

2018
PLoS One
PMCID: 5919020
PMID: 29694430
DOI: 10.1371/journal.pone.0195994

[…] oaded in http://www.bioinformatics.bbsrc.ac.uk/projects/download.html). To obtain the best assembled results, we employed two assembly software programs to assemble the genome of Z.mobilis, including Edena V3 [] and Velvet [].These scaffolds were ordered relative to the genome of the Z. mobilis strain ZM4, using a combination of the Contiguator [] and ACT 10.2.0 []. The Illumina reads were remappe […]

library_books

Genomic Structural Variations Affecting Virulence During Clonal Expansion of Pseudomonas syringae pv. actinidiae Biovar 3 in Europe

2018
Front Microbiol
PMCID: 5895724
PMID: 29675009
DOI: 10.3389/fmicb.2018.00656

[…] ference based assemblies of relatively small DNA regions such as PAC_ICE2, and for the assembly of unmapped reads for gene discovery, the Illumina reads of the 12 European strains were processed with Edena (Hernandez et al., ). From the same datasets, full genomes were drafted with SPAdes (Bankevich et al., ) and scaffolded with Ragout (Kolmogorov et al., ) having the complete genome of CRAFRU 14. […]

library_books

A Comprehensive Study of De Novo Genome Assemblers: Current Challenges and Future Prospective

2018
Evol Bioinform Online
PMCID: 5826002
PMID: 29511353
DOI: 10.1177/1176934318758650

[…] %.On single-end prokaryotic data sets, Velvet showed second highest genome fraction with mean of 59.6% followed by Perga with third highest genome fraction with mean of 57.6%, whereas Ray, SSAKE, and Edena showed average accuracy with mean genome fraction of 48.7%, 44.3%, and 43.8%. On eukaryotic paired-end data sets, Edena showed highest genome fraction with a mean of 90.4% and the second highest […]

library_books

Draft Genome Sequences of Escherichia coli Isolates from India

2018
Genome Announc
PMCID: 5814501
PMID: 29449387
DOI: 10.1128/genomeA.00047-18

[…] m. Two million paired-end reads for each strain were obtained upon filtering the data for quality and size using Prinseq-lite. De novo assembly was done using CLC Genomics Workbench version 6.0.1 and Edena version 3.13 to generate contigs. The contigs obtained from these assemblers were integrated using the Contig Integrator for Sequence Assembly (CISA). This yielded 136 and 179 contigs for Escher […]

library_books

Inferences on specificity recognition at the Malus×domestica gametophytic self incompatibility system

2018
Sci Rep
PMCID: 5788982
PMID: 29379047
DOI: 10.1038/s41598-018-19820-1

[…] 18 transcriptomes were estimated using Express as implemented in Trinity (default parameters). The reads were then used in the transcriptome assembly using Trinity (default parameters) and also using Edena with the following K-mer values 20, 25, 30, 35, 40, 45, 50, 55 and 60. Assembly statistics for both assemblies were obtained with ABySS 2.0 (Supplementary Table  and Supplementary Table ). The r […]

library_books

The Novel Phages phiCD5763 and phiCD2955 Represent Two Groups of Big Plasmidial Siphoviridae Phages of Clostridium difficile

2018
Front Microbiol
PMCID: 5786514
PMID: 29403466
DOI: 10.3389/fmicb.2018.00026

[…] nce assemblies are required to corroborate this statement. It is unlikely that this third group of big phage corresponds to sequence artifacts, as we observed them in high-coverage WGS assembled with edena, SPAdes and a5 (coverage 140–300X, data not shown) and more recently in a Illumina and PacBio sequences for three Clade C-I isolates from Costa Rica (unpublished results). The correspondence of […]

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Edena institution(s)
Genomic Research Laboratory, Infectious Diseases Service, Geneva University Hospitals, Geneva, Switzerland; Scripps Translational Science Institute, The Scripps Research Institute, La Jolla, CA, USA; BioMérieux, Data and Knowledge Laboratory, Marcy l’Etoile, France; Fasteris SA, Plan-les-Ouates, Switzerland
Edena funding source(s)
Supported by Swiss National Science Foundation (3100A0-112370/1).

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