Single-base mismatch profiles for NGS samples

TL;DR

This paper introduces a method to analyze the relationship between single-base mismatch profiles in NGS samples and the biological nature of the samples, using similarity measures to compare these profiles.

Contribution

It presents a novel approach to characterize NGS samples through Single Base Indicator matrices and introduces similarity measures to relate these profiles to biological sample types.

Findings

Strong correlation between SBI profiles and sample biology under consistent tech conditions

Proposes similarity measures for comparing SBIs effectively

Provides a new blueprint for NGS sample preprocessing analysis

Abstract

Within the preprocessing pipeline of a Next Generation Sequencing sample, its set of Single-Base Mismatches is one of the first outcomes, together with the number of correctly aligned reads. The union of these two sets provides a 4x4 matrix (called Single Base Indicator, SBI in what follows) representing a blueprint of the sample and its preprocessing ingredients such as the sequencer, the alignment software, the pipeline parameters. In this note we show that, under the same technological conditions, there is a strong relation between the SBI and the biological nature of the sample. To reach this goal we need to introduce a similarity measure between SBIs: we also show how two measures commonly used in machine learning can be of help in this context.