CEGMA pipeline

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

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Documentation


Publications for Core Eukaryotic Genes Mapping Approach

CEGMA citations

 (12)
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 […]

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. […]

2016
PMCID: 4759075

[…] with a total assembly length of 37.97 mbp (n50, 417,961 bp; n90, 106,959 bp), 49.00% g+c content, and a maximum scaffold size of 1,198,811 bp. the completeness of the assembly was assessed using cegma version 2.4 (10), which estimated the genome sequence to be 97.58% complete based on full and partial targets. the nuclear genome was annotated using the maker2 pipeline (11). overall, 10,944 […]

2016
PMCID: 4795655

[…] and rig-i-like receptor signaling pathways., transcriptome sequencing of d. japonica was performed on an illuminahiseq2000 platform. a total of 27,180 transcripts were obtained by trinity assembler. cegma analysis and mapping of all trimmed reads back to the assembly result showed that our transcriptome assembly covered most of the whole transcriptome. 23,888 out of 27,180 transcripts contained […]

2016
PMCID: 4898796

[…] kmer-based error correction in quake (kelley et al. 2010). the final assembly has an n50 of 74 kb and a total length of 261.9 mb (table 1). completeness of the assembly was first assessed using the cegma pipeline (parra et al. 2007). of the 248 core eukaryotic genes (cegs), 247 cegs were completely assembled in the c. calcarata genome. a combination of rna-sequencing, de novo, […]

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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