Testing assembly strategies of Francisella tularensis genomes to infer an evolutionary conservation analysis of genomic structures.

ABSTRACT:

Background

We benchmarked sequencing technology and assembly strategies for short-read, long-read, and hybrid assemblers in respect to correctness, contiguity, and completeness of assemblies in genomes of Francisella tularensis. Benchmarking allowed in-depth analyses of genomic structures of the Francisella pathogenicity islands and insertion sequences. Five major high-throughput sequencing technologies were applied, including next-generation "short-read" and third-generation "long-read" sequencing methods.

Results

We focused on short-read assemblers, hybrid assemblers, and analysis of the genomic structure with particular emphasis on insertion sequences and the Francisella pathogenicity island. The A5-miseq pipeline performed best for MiSeq data, Mira for Ion Torrent data,

SUBMITTER: Neubert K 

PROVIDER: S-EPMC8590783 | biostudies-literature | 2021 Nov

REPOSITORIES: biostudies-literature