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...

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Bibliographic Details
Published in:BioMed research international 2019, Vol.2019 (2019), p.1-12
Main Authors: Kim, Baeksop, Yoon, Jeehee, Won, Jung-Im, Huh, Sun, Kong, Jinhwa, Kim, Kiyong
Format: Article
Language:English
Subjects:
Accuracy
Algorithms
Analysis
Animals
Annotations
Assembly
Bioinformatics
Biology
Biomedical research
Case studies
Databases, Nucleic Acid
Gene expression
Gene sequencing
Genes
Genome, Helminth
Genomes
Genomic analysis
Genomics
Laboratories
Mathematical analysis
Molecular Sequence Annotation
Nucleotide sequence
Pipeline design
Researchers
Software
Studies
Toxocara canis - genetics
Whole Genome Sequencing
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Summary: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.
ISSN:2314-6133
2314-6141
DOI:10.1155/2019/4767354