GAAP: A Genome Assembly + Annotation Pipeline.
Genomic analysis begins with de novo assembly of short-read fragments in order to reconstruct full-length base sequences without exploiting a reference genome sequence. Then, in the annotation step, gene locations are identified within the base sequences, and the structures and functions of these ge...
| Publicado en: | BioMed Research International pp. 1 - 13 |
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| Autores principales: | , , , , , |
| Formato: | research tables/charts Journal Article |
| Publicado: |
Wiley-Blackwell
6/26/2019
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| Acceso en línea: | Ver este registro en EBSCOhost |
| fields | @attributes: recordID: 1 pdfLink: plink: https://search.ebscohost.com/login.aspx?direct=true&db=ccm&AN=137178390&site=ehost-live header: @attributes: shortDbName: ccm uiTerm: 137178390 longDbName: CINAHL Complete uiTag: AN controlInfo: bkinfo: dissinfo: jinfo: jid: 23146133 FT2T jtl: BioMed Research International issn: 23146133 maglogo: N pubinfo: dt: 6/26/2019 pid: 480 pub: Wiley-Blackwell place: Malden, Massachusetts artinfo: ui: 137178390 137178390 137178390 10.1155/2019/4767354 137178390 ppf: 1 ppct: 12 formats: fmt: – @attributes: type: T – @attributes: type: P tig: atl: GAAP: A Genome Assembly + Annotation Pipeline. aug: au: Kong, Jinhwa Huh, Sun Won, Jung-Im Yoon, Jeehee Kim, Baeksop Kim, Kiyong affil: Korea National Institute of Health, Cheongju 28159, Republic of Korea sug: subj: Genome Sequence Analysis Methods Genes Physiology Bioinformatics Human Genomics Algorithms Research Personnel Gene Expression Profiling Information Technology ab: Genomic analysis begins with de novo assembly of short-read fragments in order to reconstruct full-length base sequences without exploiting a reference genome sequence. Then, in the annotation step, gene locations are identified within the base sequences, and the structures and functions of these genes are determined. Recently, a wide range of powerful tools have been developed and published for whole-genome analysis, enabling even individual researchers in small laboratories to perform whole-genome analyses on their objects of interest. However, these analytical tools are generally complex and use diverse algorithms, parameter setting methods, and input formats; thus, it remains difficult for individual researchers to select, utilize, and combine these tools to obtain their final results. To resolve these issues, we have developed a genome analysis pipeline (GAAP) for semiautomated, iterative, and high-throughput analysis of whole-genome data. This pipeline is designed to perform read correction, de novo genome (transcriptome) assembly, gene prediction, and functional annotation using a range of proven tools and databases. We aim to assist non-IT researchers by describing each stage of analysis in detail and discussing current approaches. We also provide practical advice on how to access and use the bioinformatics tools and databases and how to implement the provided suggestions. Whole-genome analysis of Toxocara canis is used as case study to show intermediate results at each stage, demonstrating the practicality of the proposed method. pubtype: Academic Journal doctype: research tables/charts Journal Article ougenre: Article language: English refInfo: holdings: @attributes: islocal: N |
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