Distinguishing low frequency mutations from RT-PCR and sequence errors in viral deep sequencing data

BMC Genomics

Volumn 16, Issue 1, 2015, Pages

  Orton, Richard J ^a,b   Wright, Caroline F ^c   Morelli, Marco J ^d   King, David J ^c   Paton, David J ^c   King, Donald P ^c   Haydon, Daniel T ^a  

^a UNIVERSITY OF GLASGOW   (United Kingdom)

^b UNIVERSITY OF GLASGOW   (United Kingdom)

^c INSTITUTE FOR ANIMAL HEALTH   (United Kingdom)

^d ISTITUTO ITALIANO DI TECNOLOGIA   (Italy)

Author keywords

High throughput sequencing; Next generation sequencing; Quasispecies; Rare mutations; RT PCR errors; Sequencing error correction; Variant calling; Viral evolution; Viral population

Indexed keywords

COMPLEMENTARY DNA; DNA FRAGMENT; PLASMID DNA; SINGLE STRANDED RNA; VIRUS RNA;

ARTICLE; COMPUTER ANALYSIS; CONTROLLED STUDY; DNA FRAGMENTATION; ERROR; FOOT AND MOUTH DISEASE VIRUS; GENE AMPLIFICATION; GENETIC VARIABILITY; HIGH THROUGHPUT SEQUENCING; HISTOGRAM; MATHEMATICAL MODEL; MUTATION RATE; NEXT GENERATION SEQUENCING; NONHUMAN; NUCLEIC ACID BASE SUBSTITUTION; PREDICTION; REVERSE TRANSCRIPTION; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA ANALYSIS; SEQUENCE ERROR; SIMULATION; VIRUS EXAMINATION; VIRUS GENOME; VIRUS MUTATION; GENE FREQUENCY; GENETICS; MUTATION; RNA VIRUS; SEQUENCE ANALYSIS; STANDARDS; THEORETICAL MODEL;

RNA VIRUSES;

GENE FREQUENCY; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; MODELS, THEORETICAL; MUTATION; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA VIRUSES; RNA, VIRAL; SEQUENCE ANALYSIS, RNA;

EID: 84929082774     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/s12864-015-1456-x     Document Type: Article

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