Exodus: sequencing-based pipeline for quantification of pooled variants.

ABSTRACT:

Summary

Next-Generation Sequencing is widely used as a tool for identifying and quantifying microorganisms pooled together in either natural or designed samples. However, a prominent obstacle is achieving correct quantification when the pooled microbes are genetically related. In such cases, the outcome mostly depends on the method used for assigning reads to the individual targets. To address this challenge, we have developed Exodus-a reference-based Python algorithm for quantification of genomes, including those that are highly similar, when they are sequenced together in a single mix. To test Exodus' performance, we generated both empirical and in silico next-generation sequencing data of mixed genomes. When applying Exodus to these data, we observed median error rates varying b

SUBMITTER: Vainberg-Slutskin I 

PROVIDER: S-EPMC9191209 | biostudies-literature | 2022 Jun

REPOSITORIES: biostudies-literature