Edena protocols

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 IN pipelines

 (6)
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 (9) and edena (10) software, and multiplex pcr was used to close the gaps and remove regions of low coverage (11). the software program glimmer (12) and the rast suite (13) were used to identify […]

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) (15, 16), 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 […]

2014
PMCID: 4183865
PMID: 25278521
DOI: 10.1128/genomeA.00864-14

[…] platform using indexed paired-end 250-nucleotide v2 chemistry. the sequencing produced an output of 1,854,337 reads representing approximately 70-fold coverage of the genome. assembly, made by edena assembler (9), yielded 412 contigs with a maximum length of 150 kb and an n50 of 46 kb, assuming a genome size of 6.42 mb. the g+c content is 57.9%, which is similar to the 57.12% g+c content […]

2014
PMCID: 4263846
PMID: 25502684
DOI: 10.1128/genomeA.01308-14

[…] platform using indexed paired-end 250-nucleotide v2 chemistry. the sequencing produced an output of 778,712 reads representing approximately 40-fold coverage of the genome. assembly, made by edena assembler (7), yielded 185 contigs with a maximum length of 202 kbp and n50 of 50 kbp, assuming a genome size of 4.74 mb. the g+c content is 54.7%, which is within the range reported […]

2012
PMCID: 3399222
PMID: 22826705
DOI: 10.3389/fmicb.2012.00255

[…] usa). genomic dna was sequenced using paired-end methodology on the illumina gaii analyzer (illumina, inc., san diego, usa) by baseclear (leiden, the netherlands). the reads were assembled with edena v.2.1.1 software (hernandez et al., 2008). to construct phylogenetic tree 15 closely related vibrio type strains with 7 gene loci (16s rrna, rpoa, reca, ftsz, gapa, gyrb and mreb) were chosen. […]

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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