Computational protocol: Draft genome sequence of the extremely halophilic Halorubrum sp. SAH-A6 isolated from rock salts of the Danakil depression, Ethiopia

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Protocol publication

[…] The genome sequencing was performed using a single molecule real-time (SMRT) sequencing platform on the PacBio RS II (Pacific Biosciences, Menlo Park, CA) . Genomic DNA was extracted using a standard genomic DNA isolation kit (Promega, USA). The whole genome sequence of strain SAH-A6 was performed using single SMRT cell with a single 180 min movie (Pacific Biosciences) with P6C4 chemistry. The open reading frames of the assembled genome were predicted and annotated using the hierarchical genome-assembly process (HGAP) protocol RS HGAP Assembly 2 in SMRT analysis version 2.3.0 (Pacific Biosciences; https://github.com/PacificBiosciences/SMRT-Analysis), IMG-ER , NCBI COG function , Pfam information , and EzTaxon database. The rRNA and tRNA genes were identified using RNAmmer 1.2 and tRNA scan-SE 1.23 , respectively. The whole genome sequence of SAH-A6 was annotated using the Rapid Annotation System Technology (RAST) server. The pie chart showed the count of each subsystem feature and the subsystem coverage. […]

Pipeline specifications

Software tools SMRT-Analysis, HGAP, RNAmmer, tRNAscan-SE, RAST
Databases Pfam EzBioCloud
Applications Genome annotation, WGS analysis
Chemicals Sulfur