Ray: Simultaneous Assembly of Reads from a Mix of High-Throughput Sequencing Technologies

By Sébastien Boisvert, François Laviolette, Jacques Corbeil. J. Comput. Biol., 2010

555 citations recorded by the source corpus.

Abstract An accurate genome sequence of a desired species is now a pre-requisite for genome research. An important step in obtaining a high-quality genome sequence is to correctly assemble short reads into longer sequences accurately representing contiguous genomic regions. Current sequencing technologies continue to offer increases in throughput, and corresponding reductions in cost and time. Unfortunately, the benefit of obtaining a large number of reads is complicated by sequencing errors, with different biases being observed with each platform. Although software are available to assemble reads for each individual system, no procedure has been proposed for high-quality simultaneous assembly based on reads from a mix of different technologies. In this paper, we describe a parallel short-read assembler, called Ray, which has been developed to assemble reads obtained from a combination of sequencing platforms. We compared its performance to other assemblers on simulated and real datasets. We used a combination of Roche/454 and Illumina reads to assemble three different genomes. We showed that mixing sequencing technologies systematically reduces the number of contigs and the number of errors. Because of its open nature, this new tool will hopefully serve as a basis to develop an assembler that can be of universal utilization (availability: http://deNovoAssembler.sf.Net/). For online Supplementary Material, see www.liebertonline.com.

Subfields: Ecology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/38410204a2977a9484e6d1205697b4103b5482f7

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Ecology

In Molecular Biology

Citations in the corpus

SSPACE-LongRead: scaffolding bacterial draft genomes using long read sequence information (2014, methodology): “The user needs to create a draft assembly using a de novo assembly method of choice ( e.g. Velvet [1], SOAPdenovo [2], Ray [18], CLCbio (CLC bio, Aarhus, Denmark) or Newbler (Roche)).”
Efficient de novo assembly of large genomes using compressed data structures. (2012, unknown): “Currently available assemblers require either a single computer with very large amounts of memory—typically in the hundreds of gigabytes (Li et al. 2010b; Gnerre et al. 2011)—or a large distributed cluster of tightly coupled computers (Simpson et al. 2009; Boisvert et al. 2010).”
Assembling Single-Cell Genomes and Mini-Metagenomes From Chimeric MDA Products (2013, unknown): “In particular, we show that it improves on A5 (Tritt et al., 2012), ABySS ASSEMBLING SINGLE CELL GENOMES AND MINI-METAGENOMES (Simpson et al., 2009), CLC, 1 EULER-SR (Chaisson et al., 2009), Ray (Boisvert et al., 2010), SOAPde-novo (Li et al., 2010), and Velvet (Zerbino and Birney, 2008) in multicel”
Next generation sequencing and bioinformatic bottlenecks: the current state of metagenomic data analysis. (2012, background): “Assembly RAY [44] Velvet [21] SOAPdenovo [45] Newbler [20] ABySS [46] ALLPATHs [16] Genovo [24] CLCbio http://clcbio.”
Assembling Genomes and Mini-metagenomes from Highly Chimeric Reads (2013, background): “) In particular, we show that it improves on A5 [13], ABySS [14], CLC, EULER-SR [15], Ray [16], SOAPdenovo [17]), and Velvet [18] in multicell bacterial assemblies.”
Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species (2013, methodology): “It should also be noted that the Ray assembler [60] that was used for the Ray fish assembly, was designed to work with Illumina and Roche 454 reads, but this team chose to only use the Illumina data in their assembly.”