A Pipeline for Constructing Reference Genomes for Large Cohort-Specific Metagenome Compression.

ABSTRACT: Metagenomic data compression is very important as metagenomic projects are facing the challenges of larger data volumes per sample and more samples nowadays. Reference-based compression is a promising method to obtain a high compression ratio. However, existing microbial reference genome databases are not suitable to be directly used as references for compression due to their large size and redundancy, and different metagenomic cohorts often have various microbial compositions. We present a novel pipeline that generated simplified and tailored reference genomes for large metagenomic cohorts, enabling the reference-based compression of metagenomic data. We constructed customized reference genomes, ranging from 2.4 to 3.9 GB, for 29 real metagenomic datasets and evaluated their compression p

SUBMITTER: Wang L 

PROVIDER: S-EPMC10609127 | biostudies-literature | 2023 Oct

REPOSITORIES: biostudies-literature