Libra: scalable k-mer-based tool for massive all-vs-all metagenome comparisons.

ABSTRACT:

Background

Shotgun metagenomics provides powerful insights into microbial community biodiversity and function. Yet, inferences from metagenomic studies are often limited by dataset size and complexity and are restricted by the availability and completeness of existing databases. De novo comparative metagenomics enables the comparison of metagenomes based on their total genetic content.

Results

We developed a tool called Libra that performs an all-vs-all comparison of metagenomes for precise clustering based on their k-mer content. Libra uses a scalable Hadoop framework for massive metagenome comparisons, Cosine Similarity for calculating the distance using sequence composition and abundance while normalizing for sequencing depth, and a web-based implementation in iMicrobe (h

SUBMITTER: Choi I 

PROVIDER: S-EPMC6354030 | biostudies-literature | 2019 Feb

REPOSITORIES: biostudies-literature