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

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.

Repeated replacement of an intrabacterial symbiont in the tripartite nested mealybug symbiosis

“…Read error correction (BayesHammer), de novo assembly (k-mers K21, K33, K55, and K77 for 100-bp data and K99 and K127 for 300-bp data), and mismatch/short-indel correction were performed by the SPAdes assembler, v3.5.0 (83). Additional endosymbionttargeted long k-mer (91 and 241 bp) assemblies generated by the Ray v2.3.1 (84) and PRICE v1.2 (85) assemblers were used to improve assemblies of complex endosymbiont regions.…”

Outlier analyses to test for local adaptation to breeding grounds in a migratory arctic seabird

“…The proportion of usable pairs was between 34 and 36% for all read sets. We assembled the preprocessed reads to create a first set of consensus sequences using the assembler implemented in ray v.2.3.0 (Boisvert, Laviolette, & Corbeil, 2010). After reviewing assembly statistics and coverage statistics for various k‐mer sizes, K  =   31 was chosen for the definitive assembly.…”

The genome of an Encephalitozoon cuniculi type III strain reveals insights into the genetic diversity and mode of reproduction of a ubiquitous vertebrate pathogen

“…Sequencing resulted in 28 870 687 pairs of paired-end reads with a Q30 of 92.62%. Reads were assembled in parallel with the SPAdes v3.5.0 assembler (Bankevich et al, 2012) as well as with the Ray v2.3.1 assembler (Boisvert et al, 2010), and the resulting assemblies manually inspected and merged using the overlap-layout-consensus algorithm implemented in Geneious Pro version R8.1.2 (http://www.geneious.com, Kearse et al, 2012). The final assembly size reaches 2.3 Mb, and is separated into 15 contigs with an N50 of 201956 bp.…”

“…Initially, we used Ray denovo assembler v2.3.1 (Boisvert et al, 2010) with a k value of 123 to generate contiguous sequences. Contigs were validated by comparing with existing E. cuniculi assemblies, as well as by mapping paired-end reads back to them using mapping algorithms implemented in Geneious Pro.…”