GENOMICON-Seq: A comprehensive tool for the simulation of mutations in amplicon and whole exome sequencing

Author:

Stosic Milan S.ORCID,Costanzi Jean-MarcORCID,Ambur Ole HermanORCID,Rounge Trine B.ORCID

Abstract

AbstractGENOMICON-Seq is a comprehensive genomic sequencing simulation tool that enables the assessment of laboratory and bioinformatics parameters influencing the detection of mutations. The tool generates genomes with mutations, mimicking processes such as low-frequency mutations, APOBEC3 activity in viruses, somatic mutations and single base substitution (SBS) mutational signals. GENOMICON-Seq adds amplicon and whole exome sequencing biases and errors. It outputs sequencing reads compatible with mutation detection tools and a report on mutation origin (generated mutations and PCR errors), nucleotide context, and position. GENOMICON-Seq aids in the evaluation of bioinformatics tools and experimental designs, reducing the need for costly real-world sequencing experiments.

Publisher

Cold Spring Harbor Laboratory

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