EuGene-PP specifications

Information


Unique identifier OMICS_04224
Name EuGene-PP
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data EuGene-PP can run using just FASTA genomic sequences and expression data (provided as oriented Single/Pair-end reads in either FASTQ/FASTA format, mapped reads in Bam/Sam, Bed or Wig format, or tiling array data in ndf/pair files).
Operating system Unix/Linux
Computer skills Advanced
Version 1.1
Stability Stable
Maintained Yes

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Publication for EuGene-PP

EuGene-PP in publications

 (3)
PMCID: 5577687
PMID: 28854875
DOI: 10.1186/s12864-017-4087-6

[…] strain to achieve ~100× coverage. de novo assembling was performed using hgap assembler [] version 3.0 (pacific biosciences, menlo park, ca). annotation of whole genome assemblies was performed with eugene-pp version 1.2 automated pipeline [], using swiss-prot as protein and training protein databases (http://www.uniprot.org/). the sequences of tal genes were manually retrieved using blastn […]

PMCID: 5036818
PMID: 27669415
DOI: 10.1371/journal.pone.0163729

[…] using soapdenovo 1.05 [] and velvet 1.2.02 []. the assemblies had a total length of 5.06 mb generating 77 contigs. the g+c content of the sequence was of 65.42%. annotation was performed using eugene-pp using similarities with known protein sequences []. annotation of the genome sequences revealed 4337 putative protein-coding sequences, 55 trna, and three rrna., in a first step 26 tr loci […]

PMCID: 4686621
PMID: 26734033
DOI: 10.3389/fpls.2015.01126

[…] 1.05 (li et al., ) and velvet 1.2.02 (zerbino and birney, ). then contigs were scaffolded with lynx (gouzy, unpublished data) using mate-pair read information. annotation was performed using eugene-pp using similarities with known protein sequences (sallet et al., ). a probably non-exhaustive list of known t3es that were previously identified in various pathogenic bacteria genus […]


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EuGene-PP institution(s)
Laboratoire Interactions Plantes Micro-organismes (LIPM) UMR441/2594, INRA/CNRS, France; INRA, Unité de Mathématiques et Informatique Appliques de Toulouse, UR 875, Castanet-Tolosan, France
EuGene-PP funding source(s)
This work was supported by the Agence Nationale de la Recherche ANR-08-GENO-106 grant ‘SYMbiMICS’, in TULIP LabEx (ANR-10-LABX-41).

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