Exploring single-sample SNP and INDEL calling with whole-genome de novo assembly

• Published in: Bioinformatics Vol. 28; no. 14; pp. 1838 - 1844
• Main Author: Li, Heng
• Format: Journal Article
• Language: English
• Published: Oxford Oxford University Press 15.07.2012
• Subjects: Algorithms; Assembly; Biological and medical sciences; Computational Biology - methods; Construction; Fundamental and applied biological sciences. Psychology; General aspects; Graphs; Humans; INDEL Mutation; Insertion; Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects); Original Papers; Pipelines; Polymorphism, Single Nucleotide; Sequence Analysis, DNA - methods; Strings; Chromosomal aberration; Sample; Deletion; Insertion; Single nucleotide polymorphism; Genome; De novo
• ISSN: 1367-4803; 1367-4811; 1367-4811; 1460-2059
• DOI: 10.1093/bioinformatics/bts280

Motivation: Eugene Myers in his string graph paper suggested that in a string graph or equivalently a unitig graph, any path spells a valid assembly. As a string/unitig graph also encodes every valid assembly of reads, such a graph, provided that it can be constructed correctly, is in fact a lossles...