Heterozygous genome assembly via binary classification of homologous sequence

BMC Bioinformatics

Table 1 Feature values for classification of homologous contig pairs

Feature Description	Definition	Expected Value for Homologous Pair	Expected Range for Non-Homologous Pair
Length Ratio	$\frac{m i n (s e q A L e n, s e q B L e n)}{m a x (s e q A L e n, s e q B L e n)}$	≈1	0 < × ≤ 1
Depth Ratio	$\frac{m i n (s e q A D e p, s e q B D e p)}{m a x (s e q A D e p, s e q B D e p)}$	≈1	0 < × ≤ 1
% Identical Matches	pidentFromBLASTnAlignment	≈100	0 ≤ × ≪ 100
% Length Alignment	$\frac{l e n g t h F r o m B L A S T n A l i g n m e n t}{m i n (s e q A L e n, s e q B L e n)}$	≈100	0 ≤ × ≪ 100
Seq A Depth Proportion to Mode	$\frac{s e q A D e p}{M o d e O f A l l S e q u e n c e s D e p t h s}$	$\approx \frac{A v e r a g e H a p l o i d S e q u e n c e D e p t h}{M o d e O f A l l S e q u e n c e s D e p t h s}$	0 < x
Seq B Depth Proportion to Mode	$\frac{s e q B D e p}{M o d e O f A l l S e q u e n c e s D e p t h s}$	$\approx \frac{A v e r a g e H a p l o i d S e q u e n c e D e p t h}{M o d e O f A l l S e q u e n c e s D e p t h s}$	0 < x

ISSN: 1471-2105