An overlooked phenomenon: complex interactions of potential error sources on the quality of bacterial de novo genome assemblies.

ABSTRACT:

Background

Parameters adversely affecting the contiguity and accuracy of the assemblies from Illumina next-generation sequencing (NGS) are well described. However, past studies generally focused on their additive effects, overlooking their potential interactions possibly exacerbating one another's effects in a multiplicative manner. To investigate whether or not they act interactively on de novo genome assembly quality, we simulated sequencing data for 13 bacterial reference genomes, with varying levels of error rate, sequencing depth, PCR and optical duplicate ratios.

Results

We assessed the quality of assemblies from the simulated sequencing data with a number of contiguity and accuracy metrics, which we used to quantify both additive and multiplicative effects of the four

SUBMITTER: Radai Z 

PROVIDER: S-EPMC10777565 | biostudies-literature | 2024 Jan

REPOSITORIES: biostudies-literature