An incrementally updatable and scalable system for large-scale sequence search using the Bentley-Saxe transformation.

ABSTRACT:

Motivation

In the past few years, researchers have proposed numerous indexing schemes for searching large datasets of raw sequencing experiments. Most of these proposed indexes are approximate (i.e. with one-sided errors) in order to save space. Recently, researchers have published exact indexes-Mantis, VariMerge and Bifrost-that can serve as colored de Bruijn graph representations in addition to serving as k-mer indexes. This new type of index is promising because it has the potential to support more complex analyses than simple searches. However, in order to be useful as indexes for large and growing repositories of raw sequencing data, they must scale to thousands of experiments and support efficient insertion of new data.

Results

In this paper, we show how to build a sca

SUBMITTER: Almodaresi F 

PROVIDER: S-EPMC9191210 | biostudies-literature | 2022 Jun

REPOSITORIES: biostudies-literature