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Results: 7

1.
Figure 6

Figure 6. Mock strain coverage.. From: Optimizing Read Mapping to Reference Genomes to Determine Composition and Species Prevalence in Microbial Communities.

(A). Coverage of mock strains in the MMD. This image shows the results of mapping the mock community query against the MMD under both top random and unique only mapping strategies. (B). Coverage of mock strains in the RGD. This image shows the results of mapping the mock community query against the RGD under both top random and unique only mapping strategies. The numbers printed in the plot reflect the number of strains present in the RGD for the genus in which the displayed strain belongs.

John Martin, et al. PLoS One. 2012;7(6):e36427.
2.
Figure 5

Figure 5. Mapping Resolution.. From: Optimizing Read Mapping to Reference Genomes to Determine Composition and Species Prevalence in Microbial Communities.

(A). Using a top random mapping strategy to classify at the strain or genus level. This image shows the mapping fate of all 22,735,802 mock queries when mapped to the RGD under a top random mapping strategy, falling back to genus level annotations when the strain cannot be identified. (B). Using a unique only mapping strategy to classify at the strain or genus level. This image shows the mapping fate of all 22,735,802 mock queries when mapped to the RGD under a unique only mapping strategy, falling back to genus level annotations when the strain cannot be identified. (C). Using a top random mapping strategy to classify at the strain or species level. This image shows the mapping fate of all 22,735,802 mock queries when mapped to the RGD under a top random mapping strategy, falling back to species level annotations when the strain cannot be identified. (D). Using a unique only mapping strategy to classify at the strain or species level. This image shows the mapping fate of all 22,735,802 mock queries when mapped to the RGD under a unique only mapping strategy, falling back to species level annotations when the strain cannot be identified.

John Martin, et al. PLoS One. 2012;7(6):e36427.
3.
Figure 3

Figure 3. Phylogenetic tree view of MMD strains and amended MMD strains based on 16S genes.. From: Optimizing Read Mapping to Reference Genomes to Determine Composition and Species Prevalence in Microbial Communities.

This image displays a phylogenetic tree based on 16S data for all 21 strains in the MMD, and also the 4 strains used as replacements in the amended MMD (D. geothermalis, Helicobacter hepaticus, Neisseria gonorrheae and Escherichia fergusonii). The shaded regions indicate the genera containing the amended strains (yellow: Escherichia, blue: Neisseria, red: Helicobacter, brown: Streptococcus and green: Deinococcus).

John Martin, et al. PLoS One. 2012;7(6):e36427.
4.
Figure 2

Figure 2. Parameter effects on mapping against the MMD and the amended MMD.. From: Optimizing Read Mapping to Reference Genomes to Determine Composition and Species Prevalence in Microbial Communities.

This plot shows the percent of total mock queries able to be mapped to the mock database at each given CLC parameter combination. The Mock vs. Mock data (dark blue) uses the original MMD, which contains all strains present in the mock community. The Mock vs. Amended data (light blue) shows the same results when the mock query is mapped to an amended MMD where several strains were removed and other strains from the same genus were included in their place.

John Martin, et al. PLoS One. 2012;7(6):e36427.
5.
Figure 1

Figure 1. Reference Genome Database creation.. From: Optimizing Read Mapping to Reference Genomes to Determine Composition and Species Prevalence in Microbial Communities.

An overview of the process of creating our Reference Genome Database (RGD). Complete and WGS genomes were downloaded from GenBank, plasmid sequences were removed to simplify redundancy screening, and then the Mauve genome assembly tool was used to identify redundant strains that were subsequently removed (except for HMP stains which were always kept). For strains remaining after redundancy removal, their corresponding plasmids were restored into the database. This database was periodically updated as new strains became available over the course of the project.

John Martin, et al. PLoS One. 2012;7(6):e36427.
6.
Figure 7

Figure 7. The effect of strain representation within the RGD and mapping strategy on mapping resolution.. From: Optimizing Read Mapping to Reference Genomes to Determine Composition and Species Prevalence in Microbial Communities.

(A). Top 20 most covered strains from the genus Bacillus found in mock vs. RGD mapping. This figure shows the detected coverage using both mapping strategies when aligning the mock community queries against the full RGD for Bacillus strains. Note that the strain present in the mock community (B. cereus ATCC 10987) is indicated in the image. (B). Top 20 most covered strains from the genus Clostridium found in mock vs. RGD mapping. This figure shows the detected coverage using both mapping strategies when aligning the mock community queries against the full RGD for Clostridium strains. Note that the strain present in the mock community (C. beijerinckii NCIMB 8052) is indicated in the image. (C). Top 20 most covered strains from the genus Bacteroides found in mock vs. RGD mapping. This figure shows the detected coverage using both mapping strategies when aligning the mock community queries against the full RGD for Bacteroides strains. Note that the strain present in the mock community (B. vulgatus ATCC 8482) is indicated in the image. (D). Top 20 most covered strains from the genus Escherichia found in mock vs. RGD mapping. This figure shows the detected coverage using both mapping strategies when aligning the mock community queries against the full RGD for Escherichia strains. Note that the strain present in the mock community (E. coli K-12 MG1655) is indicated in the image.

John Martin, et al. PLoS One. 2012;7(6):e36427.
7.
Figure 4

Figure 4. A comparison of mock and amended MMD depth of coverage.. From: Optimizing Read Mapping to Reference Genomes to Determine Composition and Species Prevalence in Microbial Communities.

This plot shows the log transformed depth values for the mock query versus the amended MMD on the y-axis, and the mock query versus the original MMD on the x-axis. Unaffected genera should lie along the diagonal, while those showing a change in depth of coverage will fall off the diagonal. The amended genera are indicated, and the 4 that were swapped do stand off the diagonal. The genus Streptococcus was represented by 3 strains in the mock community, and was amended by removing two of the three strains leaving only S. mutans UA159 in the amended MMD. The depth value of this multi-strain genus was the read normalized average value of the 3 member strains, and after being pruned down to a single strain, the single strain depth remained similar to the original, averaged value.

John Martin, et al. PLoS One. 2012;7(6):e36427.

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