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Complete genome sequence of <i>Bacillus subtilis</i> SNUY1, a novel strain enhancing antifungal activity in edible coatings. [PDF]

Microbiol Resour Announc
Yang GM, Kim NY, Song Y, Chung D, Kim HJ.   +4 more
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Error analysis of the PacBio sequencing CCS reads

The International Journal of Biostatistics, 2023
Abstract Third generation sequencing technologies such as Pacific Biosciences and Oxford Nanopore provide faster, cost-effective and simpler assembly process generating longer reads than the ones in the next generation sequencing. However, the error rates of these long reads are higher than those of the short reads, resulting in an error
Pourmohammadi, Reza, Abouei, Jamshid, Anpalagan, Alagan   +2 more
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PacBio-Based Protocol for Bacterial Genome Assembly

2021
Acquisition of high-quality bacterial genomes is fundamental, while having in mind investigation of subtitle intraspecies variation in addition to development of sensitive species-specific tools for detection and identification of the pathogens. In this view, Pacific Biosciences technology seems highly tempting taking into consideration over 10,000 bp ...
Agata, Motyka-Pomagruk, Sabina, Zoledowska, Michal, Kabza, Ewa, Lojkowska   +3 more
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Illumina, PacBio part ways

C&EN Global Enterprise, 2020
Faced with resistance from antitrust authorities concerned about reduced competition, Illumina has dropped plans to acquire its next-generation DNA-sequencing (NGS) rivalPacific Biosciences of Cali...
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Structural variation discovery in wheat using PacBio high-fidelity sequencing

The Plant Journal, 2023
AbstractBackgroundStructural variations (SVs) pervade plant genomes and contribute substantially to the phenotypic diversity. However, most SVs were ineffectively assayed because of their complex nature and the limitations of early genomic technologies.
Zhiliang Zhang, Jijin Zhang, Lipeng Kang, Xuebing Qiu, Song Xu, Jun Xu, Yafei Guo, Zelin Niu, Beirui Niu, Aoyue Bi, Xuebo Zhao, Daxing Xu, Jing Wang, Changbin Yin, Fei Lu   +14 more
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PacBio for Haplotyping in Gene Families

2017
The throughput and read length provided by Pacific Bioscience (PacBio) Single Molecule Real Time (SMRT) sequencing platform makes it feasible to construct contiguous, non-chimeric sequences. This is especially useful for genes with repetitive sequences in their gene bodies in gene families.
Wei, Zhang, Joachim, Messing
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2SNV: Quasispecies reconstruction from PacBio reads

2015 IEEE 5th International Conference on Computational Advances in Bio and Medical Sciences (ICCABS), 2015
Pacific Biosciences (PacBio) sequencing is providing thousands of reads with the length up to 10,000 bases. In most cases this length is enough to cover entire region of interest however this technology has high (≈15%) error rate. We propose a method for viral haplotype reconstruction using long SMRT reads.
Alexander Artyomenko, Nicholas C. Wu, Serghei Mangul, Eleazar Eskin, Ren Sun, Alex Zelikovsky   +5 more
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Inversion detection using PacBio long reads

2017 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 2017
Structural variation is important in disease etiology and ecological adaptation. Prior work has focused on using either only short paired-end reads or a hybrid approach that combines long and short reads to detect structural variants. Few methods have focused solely on using long reads.
Shenglong Zhu, Scott J. Emrich, Danny Z. Chen   +2 more
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Informatics for PacBio Long Reads

2019
In this article, we review the development of a wide variety of bioinformatics software implementing state-of-the-art algorithms since the introduction of SMRT sequencing technology into the field. We focus on the three major categories of development: read mapping (aligning to reference genomes), de novo assembly, and detection of structural variants.
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Bifidobacterium Genome Assembly and Methylome Analysis Using Pacbio SMRT Sequencing

2021
In this chapter, we present a generic method to achieve de novo genome assembly and methylome analysis of Bifidobacterium genomes using the Pacbio SMRT sequencing and SMRT Link pipeline. The methods described here cover the de novo Pacbio or hybrid Illumina-Pacbio assembly ideally intended to obtain a complete genome sequence, followed by the detection
Francesca, Bottacini, Douwe, van Sinderen   +1 more
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