Plantagora: Modeling Whole Genome Sequencing and Assembly of Plant Genomes

Abstract

BackgroundGenomics studies are being revolutionized by the next generation sequencing technologies, which have made whole genome sequencing much more accessible to the average researcher. Whole genome sequencing with the new technologies is a developing art that, despite the large volumes of data that can be produced, may still fail to provide a clear and thorough map of a genome. The Plantagora project was conceived to address specifically the gap between having the technical tools for genome sequencing and knowing precisely the best way to use them.Methodology/Principal FindingsFor Plantagora, a platform was created for generating simulated reads from several different plant genomes of different sizes. The resulting read files mimicked either 454 or Illumina reads, with varying paired end spacing. Thousands of datasets of reads were created, most derived from our primary model genome, rice chromosome one. All reads were assembled with different software assemblers, including Newbler, Abyss, and SOAPdenovo, and the resulting assemblies were evaluated by an extensive battery of metrics chosen for these studies. The metrics included both statistics of the assembly sequences and fidelity-related measures derived by alignment of the assemblies to the original genome source for the reads. The results were presented in a website, which includes a data graphing tool, all created to help the user compare rapidly the feasibility and effectiveness of different sequencing and assembly strategies prior to testing an approach in the lab. Some of our own conclusions regarding the different strategies were also recorded on the website.Conclusions/SignificancePlantagora provides a substantial body of information for comparing different approaches to sequencing a plant genome, and some conclusions regarding some of the specific approaches. Plantagora also provides a platform of metrics and tools for studying the process of sequencing and assembly further.

Genome of the pathogen Porphyromonas gingivalis recovered from a biofilm in a hospital sink using a high-throughput single-cell genomics platform

“…For single-cell projects, these significantly improve on traditional assemblers (designed for mono-species cultured samples), since they are able to cope with the wide variations in coverage and elevated numbers of chimeric reads and read pairs characteristic of MDA reactions. Completeness of the assemblies was assessed by using Plantagora (Barthelson et al 2011) to compare with the reference. Plantagora determines ''misassembly breakpoints'' with the assumption that the data set being assembled is a sample of the reference genome.…”

Efficient high-throughput sequencing of a laser microdissected chromosome arm

“…[1]. However, repetitive elements in higher eukaryotic genomes interfere with assembly of sequence information alone into unified chromosome-scale scaffolds [2]. This obstacle is usually overcome by construction of physical or meiotic linkage maps to provide long-range contiguity.…”

Readjoiner: a fast and memory efficient string graph-based sequence assembler

“…In order to assess the quality of the assemblies delivered by the different programs, we used the script assess_assembly.pl of the Plantagora project [26]. The script aligns the contigs to the template sequence from which the reads were sampled, using the Nucmer alignment tool [27].…”

“…The quality of assemblies of simulated datasets was compared using metrics from the Plantagora project [26] and the Assemblathon 1 project [28]. In the assemblies of c22 delivered by Readjoiner , SGA and Edena there are 4 misassembled contigs.…”