Computational protocol: Genome sequencing, annotation and analysis of Salmonella enterica sub species salamae strain DMA 1

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Protocol publication

[…] Salmonella enterica subspecies salamae strain DMA-1 was isolated from mouse stool samples on 9th October, 2012, and grown in tryptone soya agar (TSA, HiMedia, Mumbai, India). Genomic DNA extraction, amplification, 16S rRNA gene sequencing, phylogenetic analysis and G+C content were performed as described previously [,]. The genome of strain Salmonella enterica, subspecies salamae strain DMA-1 was sequenced at c-CAMP, Next Generation Genomic Facility, Bengaluru, India (http://www.ccamp.res.in), using a standard run of Illumina HiSeq 1000 sequencing technology. CLC Bio Workbench v6.0.2 (CLC Bio, Aarhus, Denmark) was employed for preprocessing of the data to remove the redundant and irrelevant information. A high quality 24,334,734 vector filtered reads at approximately 497.37 times coverage were used for final assembly (at word size of 45 and bubble size of 98). This draft genome comprising 4,826,209 bp was annotated with the help of RAST (Rapid Annotation using Subsystem Technology) system [] server and RNAmmer 1.2 [] server. […]

Pipeline specifications

Software tools RAST, RNAmmer
Applications Phylogenetics, 16S rRNA-seq analysis
Organisms Mus musculus, Salmonella enterica subsp. salamae
Diseases Salmonella Infections