title: The Genomic Scrapheap Challenge; Extracting Relevant Data from Unmapped Whole Genome Sequencing Reads, Including Strain Specific Genomic Segments, in Rats.
abstract: Unmapped next-generation sequencing reads are typically ignored while they contain biologically relevant information. We systematically analyzed unmapped reads from whole genome sequencing of 33 inbred rat strains. High quality reads were selected and enriched for biologically relevant sequences; similarity-based analysis revealed clustering similar to previously reported phylogenetic trees. Our results demonstrate that on average 20% of all unmapped reads harbor sequences that can be used to improve reference genomes and generate hypotheses on potential genotype-phenotype relationships. Analysis pipelines would benefit from incorporating the described methods and reference genomes would benefit from inclusion of the genomic segments obtained through these efforts.
authors: Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), University Medical Centre Utrecht, Utrecht, The Netherlands.|Division of Gene Regulation, The Netherlands Cancer Institute, Amsterdam, The Netherlands.
authors: Robin H
authors: RH
authors: van der Weide
authors: Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), University Medical Centre Utrecht, Utrecht, The Netherlands.
authors: Marieke
authors: M
authors: Simonis
authors: Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), University Medical Centre Utrecht, Utrecht, The Netherlands.
authors: Roel
authors: R
authors: Hermsen
authors: Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), University Medical Centre Utrecht, Utrecht, The Netherlands.
authors: Pim
authors: P
authors: Toonen
authors: Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), University Medical Centre Utrecht, Utrecht, The Netherlands.
authors: Edwin
authors: E
authors: Cuppen
authors: Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), University Medical Centre Utrecht, Utrecht, The Netherlands.
authors: Joep
authors: J
authors: de Ligt
mesh_terms: D000818:Animals; D005260:Female; D016678:Genome; D023281:Genomics / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D008297:Male; D058977:Molecular Sequence Annotation; D010802:Phylogeny; D051381:Rats; D011919:Rats, Inbred Strains / Q000235:genetics*; D012015:Reference Standards; D017422:Sequence Analysis, DNA / Q000379:methods*