The Nubeam reference-free approach to analyze metagenomic sequencing reads.

ABSTRACT: We present Nubeam (nucleotide be a matrix) as a novel reference-free approach to analyze short sequencing reads. Nubeam represents nucleotides by matrices, transforms a read into a product of matrices, and assigns numbers to reads based on the product matrix. Nubeam capitalizes on the noncommutative property of matrix multiplication, such that different reads are assigned different numbers and similar reads similar numbers. A sample, which is a collection of reads, becomes a collection of numbers that form an empirical distribution. We demonstrate that the genetic difference between samples can be quantified by the distance between empirical distributions. Nubeam includes the k-mer method as a special case, but unlike the k-mer method, it is conven

SUBMITTER: Dai H 

PROVIDER: S-EPMC7545149 | biostudies-literature | 2020 Sep

REPOSITORIES: biostudies-literature