Completing bacterial genome assemblies: strategy and performance comparisons

Abstract

Determining the genomic sequences of microorganisms is the basis and prerequisite for understanding their biology and functional characterization. While the advent of low-cost, extremely high-throughput second-generation sequencing technologies and the parallel development of assembly algorithms have generated rapid and cost-effective genome assemblies, such assemblies are often unfinished, fragmented draft genomes as a result of short read lengths and long repeats present in multiple copies. Third-generation, PacBio sequencing technologies circumvented this problem by greatly increasing read length. Hybrid approaches including ALLPATHS-LG, PacBio corrected reads pipeline, SPAdes, and SSPACE-LongRead, and non-hybrid approaches—hierarchical genome-assembly process (HGAP) and PacBio corrected reads pipeline via self-correction—have therefore been proposed to utilize the PacBio long reads that can span many thousands of bases to facilitate the assembly of complete microbial genomes. However, standardized procedures that aim at evaluating and comparing these approaches are currently insufficient. To address the issue, we herein provide a comprehensive comparison by collecting datasets for the comparative assessment on the above-mentioned five assemblers. In addition to offering explicit and beneficial recommendations to practitioners, this study aims to aid in the design of a paradigm positioned to complete bacterial genome assembly.

Oxford Nanopore MinION Sequencing and Genome Assembly

“…Typical examples of hybrid assemblers are ALLPATHS-LG [51], Celera Assembler’s PacBio corrected reads pipeline (pacBioToCA [52]), SPAdes [53], and SSPACE-LongRead [32]. Assessment and evaluation on these hybrid methods have been reported by Utturkar et al [54], Liao et al [55], and Sović et al [56]. ALLPATHS-LG takes a unique approach, in that, in addition to long reads, it also incorporates Illumina paired-end reads of two libraries: one with short overlapped fragments, and one with long jumps.…”

Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes

“…Various software tools can be used to assemble the filtered raw reads into contigs [27]. It is evident that completion of genome sequences without any undetermined bases provides the best quality over a draft status of the genome assembly which results in the form of contigs.…”

Navigating Microbiological Food Safety in the Era of Whole-Genome Sequencing

“…Several assemblers have been built to work with hybrid data (i.e., PBcR), and bacterial genomes have been successfully closed by using this approach (71). However, using hybrid sequencing requires the added work of preparing two libraries, and when the appropriate amount of data is gathered by SMRT sequencing, these data independently yield better closed assemblies than hybrid data do (72). The optimal ways of combining sequencing data may shift in the future if the cost associated with PacBio sequencing declines, if the Nanopore becomes widely adopted by microbiologists, or if a separate technology that can combine high accuracy with long reads emerges.…”