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Protocols

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

Versioning


No version available

Documentation


Publications for Core Eukaryotic Genes Mapping Approach

CEGMA citations

 (453)
library_books

Comparative Genomics Reveals the Core Gene Toolbox for the Fungus Insect Symbiosis

2018
MBio
PMCID: 5954228
PMID: 29764946
DOI: 10.1128/mBio.00636-18

[…] and one was approximately 28 Mb (S. angustum and Furculomyces boomerangus). The GC (guanine-cytosine) ratios across the whole genomes range from 28% to 33%. The core eukaryotic gene mapping approach (CEGMA) recovered more than 94% of core eukaryotic genes in all four genome assemblies. The ab initio protein-coding gene prediction identified 6,519 to 7,385 genes. Detailed genome features and statis […]

library_books

Whole genome and transcriptome analysis reveal adaptive strategies and pathogenesis of Calonectria pseudoreteaudii to Eucalyptus

2018
BMC Genomics
PMCID: 5946483
PMID: 29747580
DOI: 10.1186/s12864-018-4739-1

[…] imate 213-fold sequence coverage (Additional file : Table S1). A 63.57 Mb draft genome was assembled with 507 scaffolds (>500 bp; Table ). Scaffold N50 is 1.32 Mb and the largest scaffold is 5.15 Mb. CEGMA analysis indicated that 240 out of 248 (96.7%) core eukaryotic genes were identified in the C. pseudoreteaudii genome. This suggests a high degree of completeness for the C. pseudoreteaudii geno […]

library_books

Genome Sequencing and Analysis of the Peanut B Genome Progenitor (Arachis ipaensis)

2018
Front Plant Sci
PMCID: 5943715
PMID: 29774047
DOI: 10.3389/fpls.2018.00604

[…] tioli et al., ).The gene coverage of the assembled genome was comprehensively evaluated using available public transcript sequence tags or expressed sequence tags. Core eukaryotic genes identified by CEGMA v.2.3 (Parra et al., ) were remapped to the A. ipaensis genome assembly by BLAT (Kent, ) to evaluate the quality of the assembly. CEGMA data were downloaded from the Korf Lab research group at t […]

library_books

Comparative genomics of the nonlegume Parasponia reveals insights into evolution of nitrogen fixing rhizobium symbioses

2018
Proc Natl Acad Sci U S A
PMCID: 5960304
PMID: 29717040
DOI: 10.1073/pnas.1721395115

[…] s are provided in SI Appendix, Supplementary Methods). Validation of the final assemblies showed that 90–100% of the genomic reads mapped back to the assemblies (SI Appendix, Table S4), and 94–98% of CEGMA () and BUSCO () genes were detected (SI Appendix, Table S5). […]

library_books

Adaptations in energy metabolism and gene family expansions revealed by comparative transcriptomics of three Chagas disease triatomine vectors

2018
BMC Genomics
PMCID: 5921304
PMID: 29699489
DOI: 10.1186/s12864-018-4696-8

[…] ssembled dataset for each species was used to identify the proportion of the core eukaryotic genome coverage, as described []. We used HMM profiles for 458 core eukaryotic proteins as provided by the CEGMA dataset [] and HMMER3 searches with the hmmscan command and the -T 40 and --domT 40 filters, as described in []. Following the same approach, a Benchmarking Universal Single-Copy Orthologs (BUSC […]

library_books

Comparative genomics of bdelloid rotifers: Insights from desiccating and nondesiccating species

2018
PLoS Biol
PMCID: 5916493
PMID: 29689044
DOI: 10.1371/journal.pbio.2004830

[…] arly utilised. A final round of assembly ‘polishing’ was performed using Redundans v0.12b [], and scaffolds less than 200 bases in length were discarded. Assembly completeness was evaluated using the CEGMA v2.5 [] and BUSCO v3.0.0 [] gene sets, choosing the Eukaryota (n = 303) and Metazoa (n = 978) databases in the latter case and increasing the search limit to 8. Alternative assemblies were also […]

Citations

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

CEGMA review

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Michael Gribskov

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Desktop
CEGMA is no longer in development. Use BUSCO instead.