title: Finding Pathogenic Nucleic Acid Sequences in Next Generation Sequencing Data.
abstract: Viruses and bacteria are established as one of the main causes of human diseases from hepatitis to cancer. Recently, the presence of such pathogens has been extensively studied using human whole genome and transcriptome sequencing data. However, detecting and studying pathogens via next generation sequencing data is a challenging task in terms of time and computational resources. In this protocol we give instructions for a simple and quick method to find pathogenic DNA or RNA and detect possible integration of the pathogen genome into the host genome.
authors.affiliation: Department of Genetics, Harvard Medical School, Boston, Massachusetts.
authors.forename: Michael
authors.initials: M
authors.lastname: Parfenov
authors.affiliation: Department of Genetics, Harvard Medical School, Boston, Massachusetts.
authors.forename: J G
authors.initials: JG
authors.lastname: Seidman
mesh_terms: D001483:Base Sequence; D019295:Computational Biology / Q000379:methods*; D030561:Databases, Nucleic Acid; D064351:Genes, Microbial; D064349:Genome, Microbial; D023281:Genomics / Q000379:methods; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software
keywords: bacteria; detection; integration; next generation sequencing; pathogens; viruses