The NCBI Eukaryotic Genome Annotation Pipeline statistics

Tool stats & trends

Looking to identify usage trends or leading experts?

Protocols

The NCBI Eukaryotic Genome Annotation Pipeline specifications

Information


Unique identifier OMICS_23598
Name The NCBI Eukaryotic Genome Annotation Pipeline
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Version 7.4
Stability Stable
Maintained Yes

Versioning


No version available

The NCBI Eukaryotic Genome Annotation Pipeline citations

 (12)
library_books

Convergent genomic signatures of domestication in sheep and goats

2018
Nat Commun
PMCID: 5840369
PMID: 29511174
DOI: 10.1038/s41467-018-03206-y

[…] EP) annotations that were generated from the Ensembl v74 sheep OARv3.1 genome annotation for Ovis (http://www.ensembl.org/Ovis_aries/Tools/VEP) and from the goat CHIR1.0 genome annotation produced by the NCBI eukaryotic genome annotation pipeline for Capra (https://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/). SNPs were classified as intergenic, upstream and downstream (including UTRs), an […]

library_books

The genome of Austrofundulus limnaeus offers insights into extreme vertebrate stress tolerance and embryonic development

2018
BMC Genomics
PMCID: 5819677
PMID: 29463212
DOI: 10.1186/s12864-018-4539-7

[…] present in the assembly, 1.6% are duplicated, 12% are fragmented, and 11% are missing (TableĀ ). This draft assembly Austrofundulus limnaeus 1.0 (GenBank accession GCA_001266775.1) was annotated using the NCBI Eukaryotic Genome Annotation Pipeline. A total of 9.3 billion RNA-seq reads were aligned to the A. limnaeus genome at an average alignment frequency of 73%. This automated pipeline was able t […]

library_books

Analysis of the Aedes albopictus C6/36 genome provides insight into cell line utility for viral propagation

2018
GigaScience
PMCID: 5869287
PMID: 29329394
DOI: 10.1093/gigascience/gix135

[…] apping technologies including Hi-C, Dovetail, and BioNano technologies (reviewed in []), would be able to make use of our contigs. The contigs are publicly available, with gene annotation provided by the NCBI Eukaryotic Genome Annotation Pipeline. C6/36 joins CHO [,,] and HeLa [] as another cell line to have its genome de novo assembled. The accuracy of the assembly is supported by several observa […]

library_books

The cacao Criollo genome v2.0: an improved version of the genome for genetic and functional genomic studies

2017
BMC Genomics
PMCID: 5603072
PMID: 28915793
DOI: 10.1186/s12864-017-4120-9

[…] he transfer. For the remaining non-transferred genes, we used Exonerate (cdna2genome model), with the same selection criteria.Furthermore, a new de novo RefSeq structural annotation, was performed by the NCBI Eukaryotic Genome Annotation Pipeline with the methodology described here https://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/.Functional annotation was performed with Blastp for each […]

library_books

Genome assembly and transcriptome resource for river buffalo, Bubalus bubalis (2n = 50)

2017
GigaScience
PMCID: 5737279
PMID: 29048578
DOI: 10.1093/gigascience/gix088

[…] Annotation of genes, transcripts, and proteins was done using the NCBI Eukaryotic Genome Annotation Pipeline []. The NCBI pipeline operates on a RefSeq copy of the submitted assembly and produces RefSeq transcript and protein models, which are tracked with NCBI […]

library_books

Whole Genome Sequencing of the Braconid Parasitoid Wasp Fopius arisanus, an Important Biocontrol Agent of Pest Tepritid Fruit Flies

2017
PMCID: 5555450
PMID: 28584080
DOI: 10.1534/g3.117.040741

[…] Structural and functional annotation of genes was performed with the NCBI Eukaryotic Genome Annotation Pipeline. This automated annotation pipeline utilized transcript evidence from existing RNA-seq data for F. arisanus () in addition to NCBI RefSeq protein sets fo […]

Citations

Looking to check out a full list of citations?

The NCBI Eukaryotic Genome Annotation Pipeline reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review The NCBI Eukaryotic Genome Annotation Pipeline