The NCBI Eukaryotic Genome Annotation Pipeline protocols

View The NCBI Eukaryotic Genome Annotation Pipeline computational protocol

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The NCBI Eukaryotic Genome Annotation Pipeline specifications

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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

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The NCBI Eukaryotic Genome Annotation Pipeline in pipeline

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

[…] using a de novo transcriptome assembly pipeline based on the trinity software [], which gave 163k unique sequences across all tissues., 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 […]


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The NCBI Eukaryotic Genome Annotation Pipeline in publications

 (13)
PMCID: 5840369
PMID: 29511174
DOI: 10.1038/s41467-018-03206-y

[…] 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), […]

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

[…] in the assembly, 1.6% are duplicated, 12% are fragmented, and 11% are missing (table ). 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 […]

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

[…] 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 […]

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

[…] using a de novo transcriptome assembly pipeline based on the trinity software [], which gave 163k unique sequences across all tissues., 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 […]

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

[…] = true.” kmer based error correction of the fragment library was performed prior to assembly as part of the allpaths-lg pipeline., 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 […]


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