Computational protocol: Porphyromonas gingivalis Type IX Secretion Substrates Are Cleaved and Modified by a Sortase-Like Mechanism

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Protocol publication

[…] P. gingivalis W50ABK*WbaP was grown to stationary phase in supplemented Brain Heart Infusion medium, harvested by centrifugation and washed in 10 mM Tris-HCl pH 8.0. DNA was extracted using the Blood and Tissue Genomic DNA Isolation Kit (Qiagen) and concentrated to 100 ng/μL using ethanol precipitation then resuspended in 10 mM Tris-HCl pH 8.0.Whole-genome resequencing was performed at The Australian Genome Research Facility (AGRF) using the Illumina HiSeq-2000 Platform with the CASAVA1.8.2 pipeline. Sequencing generated 8,132,274 paired-end 100 bp reads, or 1.6 GB of nucleotides in total, representing approximately 600-fold coverage of the 2.3 MB genome. Average insert size was calculated as 422 bp. To identify small indels and single-nucleotide variants, sequence reads were aligned against the P. gingivalis W83 genome (NC_002950.2), modified with the insertion of cat, tetQ and erm inactivating rgpA, rgpB and kgp respectively []. Alignments were performed using the BWA alignment tool [], SAMtools [] and Freebayes on the Galaxy platform [–]. […]

Pipeline specifications

Software tools BaseSpace, BWA, SAMtools, FreeBayes, Galaxy
Application WGS analysis
Organisms Porphyromonas gingivalis, Bacteria