EvidentialGene protocols

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EvidentialGene specifications

Information


Unique identifier OMICS_17501
Name EvidentialGene
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Input format GFF, XLS
Output format XLS
Operating system Unix/Linux, Mac OS, Windows
Programming languages Perl
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Donald Gilbert <>

Publication for EvidentialGene

EvidentialGene in pipelines

 (4)
2018
PMCID: 5843647
PMID: 29520061
DOI: 10.1038/s41467-018-03384-9

[…] noise and misassemblies, as well as snps and isoforms, we collapsed our assembly to biologically meaningful transcripts by aligning the coding regions and keeping the longest transcript, using the evidentialgene pipeline (http://arthropods.eugenes.org/evidentialgene/trassembly.html). this yielded a filtered high-quality transcriptome of 35,747 contigs with an n50 of 1839 and n10 of 4561, […]

2017
PMCID: 5421315
PMID: 28453654
DOI: 10.1093/gbe/evx082

[…] transcript contigs using trinity v2.0.6 () with default settings. all of the transcript sequences were then taken into further process of redundancy removing using the tr2aacds pipeline, from the evidentialgene package (). the pipeline selects the “best” set of de novo assembled transcripts, based on coding potential. the selected best set contained 95,631 transcript sequences. the length […]

2017
PMCID: 5592929
PMID: 28717048
DOI: 10.1534/g3.117.043737

[…] with default parameters (http://trinityrnaseq.sourceforge.net/, ). the redundancy of the assembly was reduced through processing by cd-hit (), tgicl (), and evigene (http://arthropods.eugenes.org/evidentialgene/about/evidentialgene_trassembly_pipe.html). the de novo assembled transcripts were named as ysb_ls as prefixed by the number emanated from trinity assembler., the de novo assembled […]

2015
PMCID: 4683659
PMID: 26511500
DOI: 10.1534/g3.115.021220

[…] are available from the gene expression omnibus database at ncbi (accession: gse74241)., reads were aligned to nasonia official gene set version 2 (ogs2, january 2012, http://arthropods.eugenes.org/evidentialgene/nasonia/genes/) using gsnap software v2013-02-05. reads that mapped ambiguously, i.e., to more than one feature, were discarded. annotation and gene ontology information were obtained […]


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EvidentialGene in publications

 (33)
PMCID: 5843647
PMID: 29520061
DOI: 10.1038/s41467-018-03384-9

[…] noise and misassemblies, as well as snps and isoforms, we collapsed our assembly to biologically meaningful transcripts by aligning the coding regions and keeping the longest transcript, using the evidentialgene pipeline (http://arthropods.eugenes.org/evidentialgene/trassembly.html). this yielded a filtered high-quality transcriptome of 35,747 contigs with an n50 of 1839 and n10 of 4561, […]

PMCID: 5792630
PMID: 29386535
DOI: 10.1038/s41598-018-20262-y

[…] methods examined included standard, short-read assembly approaches using trinity and clc workbench v.7.0.3 (https://www.qiagenbioinformatics.com/), followed by a meta-assembly approach using evidentialgene (https://sourceforge.net/projects/evidentialgene/) and mira. for meta-assembly of the transcriptome, a same-mixed pattern of replicate-matching was utilized (beforeraid1-beforeraid2, […]

PMCID: 5793845
PMID: 29385567
DOI: 10.1093/gbe/evy003

[…] tabular output from the searches was further run through two perl scripts, “blast92gff3.pl” with additional options -lowscore 0.0001 -alignmax 9999 -exontype exon (http://arthropods.eugenes.org/evidentialgene/evigene/scripts/blast92gff3.pl; last accessed january 14, 2018) and the “overbestgene2.pl” (http://iubio.bio.indiana.edu/gmod/tandy/perls/overbestgene2.perl; last accessed january 14, […]

PMCID: 5787247
PMID: 29373972
DOI: 10.1186/s12864-018-4451-1

[…] genome-guided assembly with trinity. these two assemblies were combined using pasa []. final optimized and cleansed transcriptome assemblies were obtained combining all soap and pasa assemblies with evidentialgene, tr2aacds perl script []. the cds sequences of the “okayset” of evidentialgene were used for the subsequent analyses and from now on are referred to as genes. assemblies are available […]

PMCID: 5905499
PMID: 29253216
DOI: 10.1093/gigascience/gix125

[…] 1) [] were also removed. transcript de novo assemblies were performed using soap-transdenovo [] and trinity de novo [] from the processed reads. the assemblies were concatenated and used as input to evidentialgene [], a comprehensive transcriptome pipeline to identify likely complete coding regions and their proteins in the final, combined, transcriptome assembly. gene modeling was carried […]


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EvidentialGene institution(s)
Environmental Genomics Group, School of Biosciences, University of Birmingham, Birmingham, UK; Department of Biology, Indiana University, Bloomington, IN, USA; Cancer Center, Department of Biostatistics and Epidemiology, Medical College of Georgia, Georgia Regents University, Augusta, GA, USA; Department of Organismic and Evolutionary Biology, and FAS Informatics Group, Harvard University, Cambridge, MA, USA; Department of Molecular Biology and Genetics, Cornell Center for Comparative and Population Genomics, Cornell University, Ithaca, NY, USA; Department of Biostatistics and Computational Biology, University of Rochester Medical School, Rochester, NY, USA; Department of Biology, University of Rochester, Rochester, NY, USA
EvidentialGene funding source(s)
This work was supported in part by the National Science Foundation (grant No. 0640462 to DGG), including genomics computational resources via TeraGrid amd XSEDE. Additional support was provided by a start-up grant by the University of Birmingham (UK) and earlier by the Center for Genomics and Bioinformatics (CGB) at Indiana University, which was supported in part by the METACyt Initiative of Indiana University, funded in part through a major grant from the Lilly Endowment, Inc. and US NIH R24 GM-084917.

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