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

Abstract

SummaryLong 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.\n\nAvailabilitySiLiCO 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.\n\nContact\n\nSupplementary informationSupplementary data are available at Bioinformatics online.