Building large updatable colored de Bruijn graphs via merging.

ABSTRACT:

Motivation

There exist several large genomic and metagenomic data collection efforts, including GenomeTrakr and MetaSub, which are routinely updated with new data. To analyze such datasets, memory-efficient methods to construct and store the colored de Bruijn graph were developed. Yet, a problem that has not been considered is constructing the colored de Bruijn graph in a scalable manner that allows new data to be added without reconstruction. This problem is important for large public datasets as scalability is needed but also the ability to update the construction is also needed.

Results

We create a method for constructing the colored de Bruijn graph for large datasets that is based on partitioning the data into smaller datasets, building the colored de Bruijn graph using

SUBMITTER: Muggli MD 

PROVIDER: S-EPMC6612864 | biostudies-literature | 2019 Jul

REPOSITORIES: biostudies-literature