Alignment candidate threshold test for read alignment. Alignment candidate threshold was tested with respect to alignment sensitivity and analysis time. a) Time needed to align 30x coverage of pool rP to 567 sequences represented in GenomeZipper dataset. b) The number of sequences positive for pool rP. Sequences covered with aligned reads at least from 80% of the length were considered as positive (i.e. represented in the pool). While alignment candidate threshold has negligible effect on alignment sensitivity, increasing hash size reduced number of positive sequences as it is getting closer to read length (100 bp).