• Genomics & Informatics
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• 제6권2호
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• pp.87-90
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• 2008

During the last four years, the pyrosequencing-based 454 platform has rapidly displaced the traditional Sanger sequencing method due to its high throughput and cost effectiveness. Meanwhile, the Sanger sequencing methodology still provides the longest reads, and paired-end sequencing that is based on that chemistry offers an opportunity to ensure accurate assembly results. In this report, we describe an optimized approach for hybrid de novo genome assembly using pyrosequencing data and varying amounts of Sanger-type reads. 454 platform-derived contigs can be used as single non-breakable virtual reads or converted to simpler contigs that consist of editable, overlapping pseudoreads. These modified contigs maintain their integrity at the first jumpstarting assembly stage and are edited by fragmenting and rejoining. Pre-existing assembly software then can be applied for mixed assembly with 454-derived data and Sanger reads. An effective method for identifying genomic differences between reference and sample sequences in whole-genome resequencing procedures also is suggested.

• Journal of Microbiology and Biotechnology
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• 제34권8호
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• pp.1617-1626
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• 2024

Various antibiotic-resistant bacteria (ARB) are known to induce repeated pulmonary infections and increase morbidity and mortality. A thorough knowledge of antibiotic resistance is imperative for clinical practice to treat resistant pulmonary infections. In this study, we used a reads-based method and an assembly-based method according to the metagenomic next-generation sequencing (mNGS) data to reveal the spectra of ARB and corresponding antibiotic resistance genes (ARGs) in samples from patients with pulmonary infections. A total of 151 clinical samples from 144 patients with pulmonary infections were collected for retrospective analysis. The ARB and ARGs detection performance was compared by the reads-based method and assembly-based method with the culture method and antibiotic susceptibility testing (AST), respectively. In addition, ARGs and the attribution relationship of common ARB were analyzed by the two methods. The comparison results showed that the assembly-based method could assist in determining pathogens detected by the reads-based method as true ARB and improve the predictive capabilities (46% > 13%). ARG-ARB network analysis revealed that assembly-based method could promote determining clear ARG-bacteria attribution and 101 ARGs were detected both in two methods. 25 ARB were obtained by both methods, of which the most predominant ARB and its ARGs in the samples of pulmonary infections were Acinetobacter baumannii (ade), Pseudomonas aeruginosa (mex), Klebsiella pneumoniae (emr), and Stenotrophomonas maltophilia (sme). Collectively, our findings demonstrated that the assembly-based method could be a supplement to the reads-based method and uncovered pulmonary infection-associated ARB and ARGs as potential antibiotic treatment targets.

• 한국컴퓨터정보학회논문지
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• 제25권8호
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• pp.1-8
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• 2020

본 논문에서는 드노보 전사체 어셈블리의 수행시간을 단축하기 위해 RNA-seq 서열을 유전자계 정보를 활용하여 여러 노드로 분산이 가능한 방법을 제시한다. 제안하는 전사체 서열 데이터 분산기법의 성능을 측정하기 위해 애기장대의 리드를 4개의 데이터 셋(전체 비분류 리드, 완전 분류 리드, 모델 분류 리드, 무작위 분류 리드)으로 구성하여 실험을 수행하였다. 전체 비분류 데이터와 비교하여 생성된 유전자 콘티그(Contig)는 95% 일치하였고 동일한 리소스들을 사용하는 단일 노드에 비해 본 연구에서 제시하는 분산환경분산 환경 기반의 어셈블리 수행시간은 4.2배 단축되었다.