Fig. 3.

Relative assignment abundancies of Mora, AugPatho2, and Pufferfish of 950,000 synthetic short 150 bp pair-end reads to 58 E. coli strains. The synthetic short reads were simulated from the three E. coli strains: 2009C-3133, SQ110, and C43(DE3). The strains listed had at least 2000 assigned reads from at least one of the algorithms. Relative assignment percentages of the final assignments from three different algorithms are represented by the different coloured bars. The real abundance levels of the strains are represented by the red dots. AugPatho2 is Pathoscope2 but with slight changes in the code to make it able to run and output results. Assignment by Pufferfish and Bowtie2 were done by choosing the primary alignment in the SAM file, while assignment by Mora and AugPatho2 was done using Pufferfish as the initial aligner. Clark and Bowtie2 were run without any additional algorithms. Mora’s assignments are closest to the real abundances