Edena protocols

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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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  • person_outline David Hernandez <>

Publication for Edena

Edena in pipelines

 (15)
2017
PMCID: 5220689
PMID: 28119858
DOI: 10.3389/fcimb.2016.00207

[…] (carlson et al., ). the dna was sequenced on an illumina hiseq 2500 platform through pe250 protocol, providing about 630x coverage. de novo assembly of sequencing reads were performed using edena (hernandez et al., ). orfs were identified and annotated with prodigal (hyatt et al., )., all reads were mapped to reference sequence using burrows-wheeler aligner (li and durbin, ). […]

2017
PMCID: 5331496
PMID: 28183756
DOI: 10.1128/genomeA.01559-16

[…] the present study, the complete genome sequence of l. plantarum cgmcc 8198 was determined by whole-genome shotgun sequencing using illumina technology. the genome was assembled using spades () and edena () software, and multiplex pcr was used to close the gaps and remove regions of low coverage (). the software program glimmer () and the rast suite () were used to identify protein-coding genes […]

2017
PMCID: 5604783
PMID: 28818910
DOI: 10.1128/genomeA.00826-17

[…] genome sequencing was performed using an illumina gaiix with a 50-bp single-end run. approximately 7.15 million reads were obtained, and the whole genome was assembled into 186 contigs using edena (), with an average coverage of 179×. the draft genome of s. mutans strain hm has an approximate size of 2.0 mb, with a g+c content of 36.7%. the genome sequence was annotated by dfast (), […]

2016
PMCID: 4891636
PMID: 27257212
DOI: 10.1128/genomeA.00398-16

[…] with 250-bp-end reads generated 6,304,876 bp, with an average g+c content of 69.1% and 259× coverage. sequence trimming (26 nucleotides from the ends) and de novo assembly were performed using edena (version 3.130110) (, ), generating 92 contigs (largest contig, 458,130 bp; n50, 135,077 bp). the draft genome was annotated using both the rapid annotations using subsystems technology (rast) […]

2016
PMCID: 5069766
PMID: 27822534
DOI: 10.1128/mSystems.00029-16

[…] were trimmed from the remaining reads. the overall quality assessment of each corrected data set was carried out using fastqc (). paired-end reads from the hiseq2000 were de novo assembled using edena v.3.131028 () and spades v.3.0.0 (). the quality of assemblies obtained by using different parametrizations was estimated by assessing the number of single-nucleotide variants (snvs) and indels […]


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Edena in publications

 (121)
PMCID: 5919020
PMID: 29694430
DOI: 10.1371/journal.pone.0195994

[…] 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 […]

PMCID: 5895724
PMID: 29675009
DOI: 10.3389/fmicb.2018.00656

[…] 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 […]

PMCID: 5888409
PMID: 29617810
DOI: 10.1093/gbe/evy059

[…] rehabilitation (cenare) (, online). whole genome sequences (wgs) for these isolates were obtained at the wellcome trust sanger institute using hiseq 2500 instruments (illumina). velvet v.1.1 () or edena v3.131028 () were used for sequence assembly and the corresponding assembly statistics are presented in the , online. to resolve the structure of some mges, the genomes of selected napcr1 […]

PMCID: 5853040
PMID: 29629327
DOI: 10.4103/jispcd.JISPCD_381_17

[…] into six test groups (n = 10 each) according to the protocol selected for post and core construction []., the length of posts utilized in all test groups was first adjusted using diamond discs (edena, au/sg, switzerland) in a low-speed handpiece to have only 3 mm extension above the flat coronal surface of each tooth. in groups 1–3, the entire bodies of the selected posts were meticulously […]

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

[…] 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 […]


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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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