Complete Genome Sequence of Klebsiella quasipneumoniae sp.203 19001
The genome was sequenced at Majorbio Cloud platform using Illumina Hiseq and Pacific Bioscience (PacBio) single-molecule real-time (SMRT) technology RS2 reads. SeqPrep (https://github.com/jstjohn/SeqPrep), trimmomatic 0.36 (5 ), Sickle 1.33 (https://github.com/najoshi/sickle) and smrtanalysis 2.3.0 were used to quality control the reads. The reads were integrated with FastqTotalHighQualityBase.jar before being assembled using canu and SPAdes. Then the gap area was filled in the assembly results with GapCloser 1.12 (6). Glimmer 3.02 (http://ccb.jhu.edu/software/glimmer/index.shtml) and GeneMarkS 4.3 (http://topaz.gatech.edu/GeneMark) were used to predict chromosomal genome and plasmid genome, respectively. Genome annotation comparative analysis was carried out using BLAST+ 2.3.0 (ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.3.0/) against Non-Redundant Protein Database (NR) (ftp://ftp.ncbi.nlm.nih.gov/blast/db/), Swiss-Prot 2017.04.10 (https://web.expasy.org/docs/swiss-prot_guideline.html), Pfam 31.0 (http://pfam.xfam.org/), evolutionary genealogy of genes: Non-supervised Orthologous Groups 4.5.1 (EggNOG) (http://eggnogdb.embl.de/#/app/home), Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEEG)