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The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
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Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...
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Diploid organisms inherit genetic material through chromosomes from both parents. Copies of the same gene are known as alleles. In most cases, both alleles are simultaneously expressed and allow various cellular processes to function optimally. If one of the alleles is missing or mutated, the expression of the other allele can compensate; however, this is not true for all genes.
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RGAAT: A Reference-based Genome Assembly and Annotation Tool for New Genomes and Upgrade of Known Genomes.

Wanfei Liu1, Shuangyang Wu2, Qiang Lin3

  • 1CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; Joint Center for Genomics Research (JCGR), King Abdulaziz City for Science and Technology and Chinese Academy of Sciences, Riyadh 11442, Saudi Arabia; Grail Scientific Co. Ltd., Shenyang 110000, China.

Genomics, Proteomics & Bioinformatics
|December 25, 2018
PubMed
Summary

A new tool, RGAAT, efficiently handles updated genome assemblies by building consensus sequences and transferring annotations. It accurately detects sequence variants and supports genome modification and comparison for various downstream analyses.

Keywords:
Genome annotationGenome assemblyGenome comparisonVariant identification

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • High-throughput sequencing accelerates genome assembly, generating numerous updated versions.
  • Managing version-dependent annotation files and public datasets is crucial for downstream analysis.
  • Existing tools face challenges in efficient consensus building and annotation transfer across genome assemblies.

Purpose of the Study:

  • To develop a flexible toolkit, RGAAT, for efficient resequencing-based consensus building and annotation updates.
  • To provide a solution for handling updated genome assemblies and compatible datasets.
  • To improve the accuracy and efficiency of variant detection and annotation transfer.

Main Methods:

  • Developed the reference-based genome assembly and annotation tool (RGAAT).
  • Implemented variant detection algorithms comparable to GATK and superior to Freebayes and SAMtools.
  • Incorporated consensus sequence building considering true allele frequency.
  • Enabled coordinate conversion and annotation file transfer between different genome assemblies.

Main Results:

  • RGAAT demonstrated high precision, specificity, and sensitivity in sequence variant detection.
  • Achieved superior precision and specificity compared to Freebayes and SAMtools.
  • Successfully transferred annotations between different genome assemblies, strains, and species, outperforming RATT.
  • Generated coordinate conversion files for reference and query genomes.

Conclusions:

  • RGAAT is an efficient and accurate toolkit for managing updated genome assemblies.
  • It facilitates downstream analysis through reliable variant detection, consensus building, and annotation transfer.
  • RGAAT supports genome modification, comparison, and coordinate conversion, offering a comprehensive solution for genomic data management.