Digital Library[ Search Result ]
A Sort and Merge Method for Genome Variant Call Format (GVCF) Files using Parallel and Distributed Computing
JinWoo Lee, Jung-Im Won, JeeHee Yoon
http://doi.org/10.5626/JOK.2021.48.3.358
With the development of next-generation sequencing (NGS) techniques, a large volume of genomic data is being produced and accumulated, and parallel and distributed computing has become an essential tool. Generally, NGS data processing entails two main steps: obtaining read alignment results in BAM format and extracting variant information in genome variant call format (GVCF) or variant call format (VCF). However, each step requires a long execution time due to the size of the data. In this study, we propose a new GVCF file sorting/merging module using distributed parallel clusters to shorten the execution time. In the proposed algorithm, Spark is used as a distributed parallel cluster. The sorting/merge process is performed in two steps according to the structural characteristics of the GVCF file in order to use the resources in the cluster efficiently. The performance was evaluated by comparing our method with the GATK"s CombineGVCFs module based on sorting and merging execution time of multiple GVCF files. The outcomes suggest the effectiveness of the proposed method in reducing execution time. The method can be used as a scalable and powerful distributed computing tool to solve the GVCF file sorting/merge problem.
AGB (Ancestral Genome Browser): A Web Interface for Browsing Reconstructed Ancestral Genomes
Daehwan Lee, Jongin Lee, Woon-Young Hong, Eunji Jang, Jaebum Kim
With the advancement of next-generation sequencing (NGS) technologies, various genome browsers have been introduced. Because existing browsers focus on comparison of the genomic data of extant species, however, there is a need for a genome browser for ancestral genomes and their evolution. In this paper, we introduce a genome browser, AGB (Ancestral Genome Browser), that displays ancestral genome data reconstructed from existing species. With AGB, it is possible to trace genomic variations that occurred during evolution in a simple and intuitive way. We explain the capability of AGB in terms of visualizing ancestral genomic information and evolutionary genomic variations. AGB is now available at http://bioinfo.konkuk.ac.kr/genomebrowser/.
Search
Journal of KIISE
- ISSN : 2383-630X(Print)
- ISSN : 2383-6296(Electronic)
- KCI Accredited Journal
Editorial Office
- Tel. +82-2-588-9240
- Fax. +82-2-521-1352
- E-mail. chwoo@kiise.or.kr