CEGMA specifications

Information


Unique identifier OMICS_08895
Name CEGMA
Alternative name Core Eukaryotic Genes Mapping Approach
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

Taxon


  • Animals
  • Fungi
  • Plants
  • Protists

Versioning


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Documentation


CEGMA articles

CEGMA citations

 (13)
2018
PMCID: 5930835

[…] in which random stop codons are likely (clc genomics workbench user manual). in contrast, orfs of the annotated transcripts had lengths (median: 570 bp) well above the overall median., cegma mapped 69% of the 458 core eukaryotic genes (79% partially), which is acceptable considering the mean abundance of 16.17 k-mers (table 1) among the h. euphorbiae transcriptome [45]. the reverse […]

2018
PMCID: 5930835

[…] to other transcriptome assemblies of non-model taxa shows a similar or even higher orf proportion (others have approximately 70% orf proportion [37, 39]), as well as a similar ohr [39, 42]. the cegma score is only slightly below lepidoptera models with full genomes available [34], suggesting that our h. euphorbiae transcriptome is a comparably solid first draft backbone. deeper sequencing […]

2017
PMCID: 5624889

[…] (50.03%)4387 (38.91%)genes with signalp (total, %)914 (10.59%)840 (11.02%)802 (9.81%)681 (8.52%)1064 (9.44%)genes with tmhmm (total, %)1536 (17.8%)1391 (18.25%)1537 (18.8%)1469 (18.37%)1752 (15.54%)cegma completeness (%)99.1398.6999.1398.2598.47busco complete or fragmented (%)97.693.698.295.989.6 , we also improved the assembly and gene prediction of the previously published genome of o. […]

2017
PMCID: 5509663

[…] length(bp)73,180,27972,709,68270,949,54264,900,86758,773,395 figure 1 , genemark-es suite used for gene prediction resulted in a total of 16830 genes. we used 248 core eukaryotic genes (cegs) using cegma pipeline to access the completeness of the genome assembly which revealed hits for 198 cegs (~80%) with complete match and 229 (~92%) with partial match. blast2go pro version 4.0.7 was used […]

2016
PMCID: 4994213

[…] identity = 90 % and coverage >90 %). our results indicate that the catfish genome assembly covered more than 90 % of gene-coding regions. subsequently, core eukaryotic genes mapping approach (cegma) software (version 2.3) [7] was employed with 248 conserved core eukaryotic genes (cegs) to assess the gene space completeness within the generated genome assembly. these results demonstrate […]

CEGMA institution(s)
UC Davis Genome Center and Department of Molecular and Cellular Biology, University of California Davis, Davis, CA, USA

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