SiLiCO: A Simulator of Long Read Sequencing in PacBio and Oxford Nanopore

SiLiCO: A Simulator of Long Read Sequencing in PacBio and Oxford Nanopore  

硅:在PacBio和牛津纳米孔长读测序的模拟器

 View ORCID ProfileEthan Alexander García Baker, Sara Goodwin, W. Richard McCombie,  View ORCID ProfileOlivia Mendivil Ramos

doi: https://doi.org/10.1101/076901

This article is a preprint and has not been certified by peer review [what does this mean?].

 

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Abstract

Summary Long read sequencing platforms, which include the widely used Pacific Biosciences (PacBio) platform and the emerging Oxford Nanopore platform, aim to produce sequence fragments in excess of 15-20 kilobases, and have proved advantageous in the identification of structural variants and easing genome assembly. However, long read sequencing remains relatively expensive and error prone, and failed sequencing runs represent a significant problem for genomics core facilities. To quantitatively assess the underlying mechanics of sequencing failure, it is essential to have highly reproducible and controllable reference data sets to which sequencing results can be compared. Here, we present SiLiCO, the first in silico simulation tool to generate standardized sequencing results from both of the leading long read sequencing platforms.

Availability SiLiCO is an open source package written in Python. It is freely available at https://www.github.com/ethanagbaker/SiLiCO under the GNU GPL 3.0 license.

长链测序平台，包括广泛使用的太平洋生物科学(PacBio)平台和新兴的牛津纳米孔平台，旨在产生超过15-20千碱基的序列片段，并已证明在识别结构变异和减轻基因组装配方面具有优势。
然而，长读测序仍然相对昂贵和容易出错，并且失败的测序运行代表了基因组学核心设施的一个重大问题。
为了定量地评估测序失败的潜在机制，必须有高度可重复和可控的参考数据集，以便对测序结果进行比较。
在这里，我们介绍了第一个在硅模拟工具生成标准化测序结果从这两个领先的长读测序平台。