Error correction and diversity analysis of population mixtures determined by NGS

Abstract

View the peer-reviewed version (peerj.com/articles/645), which is the preferred citable publication unless you specifically need to cite this preprint.Wood GR, Burroughs NJ, Evans DJ, Ryabov EV. 2014. Error correction and diversity analysis of population mixtures determined by NGS. PeerJ 2:e645 https://doi.org/10.7717/peerj.645 E r r o r c o r r e c t i o n a n d d i v e r s i t y a n a l y s i s o f p o p u l a t i o n mi x t u r e s d e t e r mi n e d b y NGST h e i mp e t u s f o r t h i s wo r k wa s t h e n e e d t o a n a l y s e n u c l e o t i d e d i v e r s i t y i n a v i r a l mi x t a k e n f r o m h o n e y b e e s ; t h e me t h o d s a r e i l l u s t r a t e d u s i n g h o n e y b e e v i r a l s a mp l e s . T h e p a p e r h a s t wo fi n d i n g s . F i r s t , a me t h o d f o r c o r r e c t i o n o f n e x t g e n e r a t i o n s e q u e n c i n g e r r o r i n t h e t o f n u c l e o t i d e d i v e r s i t y i s a s s e mb l e d . A s t a t i s t i c a l l y b a s e d e r r o r c o r r e c t i o n me t h o d i s p r e s e n t e d , wh i c h wo r k s a t t h e l e v e l o f t h e n u c l e o t i d e d i s t r i b u t i o n r a t h e r t h a n t h e l e v e l o f i n d i v i d u a l n u c l e o t i d e s . T h e me t h o d r e l i e s o n a n e r r o r mo d e l a n d a s a mp l e o f k n o wn v i r a l g e n o t y p e s t h a t i s u s e d f o r mo d e l c a l i b r a t i o n . A c o mp e n d i u m o f e x i s t i n g a n d n e w d i v e r s i t y a n a l y s i s t o o l s i s a l s o p r e s e n t e d , a l l o wi n g h y p o t h e s e s a b o u t d i v e r s i t y a n d me a n d i v e r s i t y t o b et e s t e d a n d a s s o c i a t e d c o n fi d e n c e i n t e r v a l s t o b e c a l c u l a t e d . S o f t wa r e i n b o t h E x c e l a n d Ma t l a b a n d a g u i d e a r e a v a i l a b l e a t h t t p : / / www2 . wa r wi c k . a c . u k / f a c / s c i / s y s t e ms b i o l o g y / r e s e a r c h / s o f t wa r e / , t h e Wa r wi c k Un i v e r s i t y S y s t e ms B i o l o g y Ce n t r e s o f t wa r e d o wn l o a d s i t e .P e e r J P r e P r i n t s | h t t p : / / d x . d o i . o r g / 1 0 . 7 2 8 7 / p e e r j . p r e p r i n t s . ABSTRACTThe impetus for this work was the need to analyse nucleotide diversity in a viral mix taken from honeybees; the methods are illustrated using honeybee viral samples. The paper has two findings. First, a method for correction of next generation sequencing error in the distribution of nucleotides at a site is developed. Second, a package of methods for assessment of nucleotide diversity is assembled. A statistically based error correction method is presented, which works at the level of the nucleotide distribution rather than the level of individual nucleotides. The method relies on an error model and a sample of known viral genotypes that is used for model calibration. A compendium of existing and new diversity analysis tools is also presented, allowing hypotheses about diversity and mean diversity to be tested and associated con...