title: The fast changing landscape of sequencing technologies and their impact on microbial genome assemblies and annotation.
abstract: BACKGROUND
  The emergence of next generation sequencing (NGS) has provided the means for rapid and high throughput sequencing and data generation at low cost, while concomitantly creating a new set of challenges. The number of available assembled microbial genomes continues to grow rapidly and their quality reflects the quality of the sequencing technology used, but also of the analysis software employed for assembly and annotation.
  
  
  RESULTS
  In this work, we have explored the quality of the microbial draft genomes across various sequencing technologies. We have compared the draft and finished assemblies of 133 microbial genomes sequenced at the Department of Energy-Joint Genome Institute and finished at the Los Alamos National Laboratory using a variety of combinations of sequencing technologies, reflecting the transition of the institute from Sanger-based sequencing platforms to NGS platforms. The quality of the public assemblies and of the associated gene annotations was evaluated using various metrics. Results obtained with the different sequencing technologies, as well as their effects on downstream processes, were analyzed. Our results demonstrate that the Illumina HiSeq 2000 sequencing system, the primary sequencing technology currently used for de novo genome sequencing and assembly at JGI, has various advantages in terms of total sequence throughput and cost, but it also introduces challenges for the downstream analyses. In all cases assembly results although on average are of high quality, need to be viewed critically and consider sources of errors in them prior to analysis.
  
  
  CONCLUSIONS
  These data follow the evolution of microbial sequencing and downstream processing at the JGI from draft genome sequences with large gaps corresponding to missing genes of significant biological role to assemblies with multiple small gaps (Illumina) and finally to assemblies that generate almost complete genomes (Illumina+PacBio).
authors.affiliation: DOE Joint Genome Institute, Walnut Creek, California, United States of America. KMavrommatis@lbl.gov
authors.forename: Konstantinos
authors.initials: K
authors.lastname: Mavromatis
authors.forename: Miriam L
authors.initials: ML
authors.lastname: Land
authors.forename: Thomas S
authors.initials: TS
authors.lastname: Brettin
authors.forename: Daniel J
authors.initials: DJ
authors.lastname: Quest
authors.forename: Alex
authors.initials: A
authors.lastname: Copeland
authors.forename: Alicia
authors.initials: A
authors.lastname: Clum
authors.forename: Lynne
authors.initials: L
authors.lastname: Goodwin
authors.forename: Tanja
authors.initials: T
authors.lastname: Woyke
authors.forename: Alla
authors.initials: A
authors.lastname: Lapidus
authors.forename: Hans Peter
authors.initials: HP
authors.lastname: Klenk
authors.forename: Robert W
authors.initials: RW
authors.lastname: Cottingham
authors.forename: Nikos C
authors.initials: NC
authors.lastname: Kyrpides
mesh_terms: D016680:Genome, Bacterial; D017422:Sequence Analysis, DNA / Q000295:instrumentation / Q000379:methods*; D012984:Software