Readsynth: short-read simulation for consideration of composition-biases in reduced metagenome sequencing approaches.

ABSTRACT:

Background

The application of reduced metagenomic sequencing approaches holds promise as a middle ground between targeted amplicon sequencing and whole metagenome sequencing approaches but has not been widely adopted as a technique. A major barrier to adoption is the lack of read simulation software built to handle characteristic features of these novel approaches. Reduced metagenomic sequencing (RMS) produces unique patterns of fragmentation per genome that are sensitive to restriction enzyme choice, and the non-uniform size selection of these fragments may introduce novel challenges to taxonomic assignment as well as relative abundance estimates.

Results

Through the development and application of simulation software, readsynth, we compare simulated metagenomic sequencing l

SUBMITTER: Kuster R 

PROVIDER: S-EPMC11095026 | biostudies-literature | 2024 May

REPOSITORIES: biostudies-literature