Computational protocol: Ossabaw Pigs With a PCSK9 Gain‐of‐Function Mutation Develop Accelerated Coronary Atherosclerotic Lesions: A Novel Model for Preclinical Studies

Similar protocols

Protocol publication

[…] Genomic DNA from Ossabaw 1513 was sequenced to a ×30 coverage using Illumina paired‐end sequencing. Insertions sites were identified by comparison to the reference genome. First, reads that overlap with the inserted sequence were extracted, the flanking region was identified, and the scaffold around the PCSK9 insert was reconstructed by iteratively expanding the overhanging sequence. Second, we mapped the whole genome sequence reads to the reference pig genome. Soft clipped reads (reads that are partially mapped) are then extracted and aligned to the insert sequence. By combining the results from these steps, we reconstructed all 3 flanking sequences of the PCSK9 inserts. The entire workflow is implemented using a customized python script integrating bowtie2, fastq‐extract, samtools, and mosaic., , The coordinates of the flanking sequences were mapped using BLAST against the Sscrofa11.1 reference genome from National Center for Biotechnology Information. […]

Pipeline specifications

Software tools Bowtie2, SAMtools
Application WGS analysis
Diseases Calcinosis, Coronary Artery Disease, Metabolic Diseases, Atherosclerosis