Computational protocol: Draft Genome Sequence of Gulbenkiania indica Strain HT27T (DSM 17901T) Isolated from a Sulfur Spring in India

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Protocol publication

[…] Gulbenkiania indica strain HT27T is a Gram-negative, strictly aerobic rod and motile bacterium belonging to the class Betaproteobacteria. The bacterium was isolated from a sulfur spring from Athmallik, Orissa, India (). Analysis of the whole genome will provide insight into the bacterium’s ecological functions and evolution.The draft genome of Gulbenkiania indica strain HT27T was generated at the DOE Joint Genome Institute (JGI) using the Illumina HiSeq 2000 platform (). An Illumina standard shotgun library was constructed and sequenced using the Illumina HiSeq 2000 platform, which generated 9,623,172 reads totaling 1,453.1 Mb. The filtered Illumina reads were assembled using the Velvet (), wgsim (https://github.com/lh3/wgsim), and Allpaths-LG () tools. The final draft assembly contains 23 contigs in 20 scaffolds, totaling 2.8 Mb, with an input read coverage of 258.1-fold. The largest and N50 contigs are 734.0 kb and 286.1 kb, respectively, with a G+C content of 63.0%.The genome was annotated using the JGI Microbial Genome Annotation Pipeline (). Genes were identified using the Prodigal () and GenePRIMP () programs. The tRNA, rRNA, and other noncoding RNA genes were identified by searching the genome using the tRNAscan-SE tool (), rRNA gene models built from SILVA (), and INFERNAL (http://infernal.janelia.org), respectively. The draft genome sequence has 2,713 coding sequences (CDSs), 16 pseudogenes, 59 tRNAs, 17 rRNAs and 10 other RNAs. […]

Pipeline specifications

Software tools Velvet, Wgsim, ALLPATHS-LG, Prodigal, GenePRIMP, tRNAscan-SE
Applications Genome annotation, WGS analysis
Chemicals Sulfur