Dataset Information

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 of metagenome assembly graphs, greatly improving contiguity while maintaining accuracy. We compared Fauceted resource use and assembly quality to state of the art metagenome assemblers, as well as leading resource-efficient genome assemblers. Faucet used orders of magnitude less time and disk space than the specialized metagenome assemblers MetaSPAdes and Megahit, while also improving on their memory use; this broadly matched performance of other assemblers optimizing resource efficiency-namely, Minia and LightAssembler. However, on metagenomes tested, Faucet,o outputs had 14-110% higher mean NGA50 lengths compared with Minia, and 2- to 11-fold higher mean NGA50 lengths compared with LightAssembler, the only other streaming assembler available. Availability and implementation:Faucet is available at https://github.com/Shamir-Lab/Faucet. Contact:rshamir@tau.ac.il or eranhalperin@gmail.com. Supplementary information:Supplementary data are available at Bioinformatics online.

SUBMITTER: Rozov R

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

REPOSITORIES: biostudies-literature

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Faucet: streaming de novo assembly graph construction.

Rozov Roye R Goldshlager Gil G Halperin Eran E Shamir Ron R

Bioinformatics (Oxford, England) 20180101 1

<h4>Motivation</h4>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.<h4>Results</h4>Faucet pa ...[more]

PMID: 29036597

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Project description:MotivationThere are very few methods for de novo genome assembly based on the overlap graph approach. It is considered as giving more exact results than the so-called de Bruijn graph approach but in much greater time and of much higher memory usage. It is not uncommon that assembly methods involving the overlap graph model are not able to successfully compute greater datasets, mainly due to memory limitation of a computer. This was the reason for developing in last decades mainly de Bruijn-based assembly methods, fast and fairly accurate. However, the latter methods can fail for longer or more repetitive genomes, as they decompose reads to shorter fragments and lose a part of information. An efficient assembler for processing big datasets and using the overlap graph model is still looked out.ResultsWe propose a new genome-scale de novo assembler based on the overlap graph approach, designed for short-read sequencing data. The method, ALGA, incorporates several new ideas resulting in more exact contigs produced in short time. Among these ideas, we have creation of a sparse but quite informative graph, reduction of the graph including a procedure referring to the problem of minimum spanning tree of a local subgraph, and graph traversal connected with simultaneous analysis of contigs stored so far. What is rare in genome assembly, the algorithm is almost parameter-free, with only one optional parameter to be set by a user. ALGA was compared with nine state-of-the-art assemblers in tests on genome-scale sequencing data obtained from real experiments on six organisms, differing in size, coverage, GC content and repetition rate. ALGA produced best results in the sense of overall quality of genome reconstruction, understood as a good balance between genome coverage, accuracy and length of resulting sequences. The algorithm is one of tools involved in processing data in currently realized national project Genomic Map of Poland.Availability and implementationALGA is available at http://alga.put.poznan.pl.Supplementary informationSupplementary data are available at Bioinformatics online.

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Faucet: streaming de novo assembly graph construction.

Publications

Faucet: streaming de novo assembly graph construction.

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