CLC GENOMICS WORKBENCH READS TO LOW UPDATE

This update changes the default behavior of these exporters relative to CLC Genomics Workbench 23.0.1 and 23.0.2. The availability of these genomes will enable more comprehensive analyses of nosocomial infection by B. The new option, Export reads spanning the origin of circular chromosomes as unmapped, is checked by default, making the default behavior of these exporters match that of CLC Genomics Workbench 22.x and earlier. Table 1 shows genome assembly and annotation metrics for the three isolates. Genome annotation was performed using the DDBJ Fast Annotation and Submission Tool (DFAST) pipeline v.1.1.4 with default settings ( 7). After filtering low-quality reads and quality trimming in CLC Genomics Workbench 11.0.1 (Qiagen) using default parameters, de novo assembly of high-quality paired-end reads was conducted using CLC Genomics Workbench 11.0.1 using standard settings. Libraries were prepared for MiSeq (Illumina, Inc.) sequencing according to the manufacturer’s instructions, using a NEBNext Ultra DNA library prep kit for Illumina (NEB Japan, Tokyo, Japan) with index primers from NEBNext Multiplex Oligos for Illumina (Set1 or Set2), and then sequenced using 300-bp paired-end sequencing with a MiSeq reagent kit v.3 (600 cycles). Genomic DNA was extracted from each pellet using a QIAamp DNA minikit (Qiagen, Hilden, Germany) and fragmented using an ultrasonicator to generate fragments between 300 bp and 400 bp. cereus by amplification and sequencing of the 16S rRNA genes.īacteria were grown in Luria-Bertani broth at 30☌ for 18 h and pelleted. The identity of the three isolates was confirmed to be B. Strain GTC2903 was isolated from a patient with an opportunistic infection in 1995, and strain GTC2926 was isolated from a patient blood culture in 2006. Strain ach14 was isolated in 2014 from the whole-blood culture of a patient with bacteremia, and the two GTC strains (GTC2903 and GTC2926) were isolated from different patients and were obtained from the National BioResource Project (NBRP) Center, Organization for Research and Community Development, Gifu University.

cereus isolates derived from human patients with clinical symptoms. cereus, we sequenced the genomes of three B.

To understand the genetic background of clinical isolates of B. The bacterium is also an opportunistic pathogen causing various infections, including local infections of wounds, bacteremia, septicemia, respiratory infections, and central nervous system infections ( 6). cereus is an important foodborne pathogen and can cause two different types of gastrointestinal diseases, the emetic syndrome and the diarrheal syndrome ( 5). Bacillus cereus is a facultative, anaerobic, spore-forming, Gram-positive bacterium that is commonly present in soil ( 1), in the rhizosphere of plants ( 2, 3), and as part of animal intestinal microflora ( 4).

Clc genomics workbench reads to low