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Pipeline publication

[…] more closely related to (but distinct from) S. baltica species (F. Dailey, unpublished results). Here, we report the whole-genome sequence of this strain., PacBio sequencing with 100× coverage was performed as previously described () for Shewanella sp. strain WE21. Annotation was performed by using the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) (). Additionally, the genomes were analyzed on the Rapid Annotations using Subsystems Technology (RAST) server (). Acquired antibiotic resistance genes were identified by using ResFinder version 2.1 (), virulence factors by using VirulenceFinder version 1.2 (), clustered regularly interspaced short palindromic repeat (CRISPR) arrays by using CRISPRFinder (), genomic islands by using IslandViewer version 4 (), and prophage-related sequences by using PHASTER ()., The final assembly for Shewanella sp. strain WE21 resulted in one large closed contig with a total length of 5,266,746 bp and a G+C content of 45.3%. Genome annotation resulted in 4,416 coding sequences (CDSs) plus one potential overlapping CDS, 105 tRNAs, 176 pseudogenes, and 31 rRNAs; 96.2% of the CDSs were classified as hypothetical proteins. Five prophage-like elements between 33.7 to 43.4 kb in length were detected. No virulence factors were identified in these prophage sequences. In addition, four genomic islands of 131.4 kb, 106.5 kb, 28.7 kb, and 9.2 kb, which have GC% contents of 40.6, 42.3, 38.3, and 57.9, respectively, were identified. In the first genomic island, we […]

Pipeline specifications

Software tools CRISPRFinder, IslandViewer, PHASTER
Databases ResFinder