Faucet: streaming de novo assembly graph construction.

ABSTRACT:

Motivation

We present Faucet, a two-pass streaming algorithm for assembly graph construction. Faucet builds an assembly graph incrementally as each read is processed. Thus, reads need not be stored locally, as they can be processed while downloading data and then discarded. We demonstrate this functionality by performing streaming graph assembly of publicly available data, and observe that the ratio of disk use to raw data size decreases as coverage is increased.

Results

Faucet pairs the de Bruijn graph obtained from the reads with additional meta-data derived from them. We show these metadata-coverage counts collected at junction k-mers and connections bridging between junction pairs-contain most salient information needed for assembly, and demonstrate they enable cleaning

SUBMITTER: Rozov R 

PROVIDER: S-EPMC5870852 | biostudies-literature | 2018 Jan

REPOSITORIES: biostudies-literature