Additional file 1 of Simulating metagenomic stable isotope probing datasets with MetaSIPSim
Creators: name: Barnett, Samuel
name: Buckley, Daniel
Publisher: name: figshare
Year: 2020
Subjects: subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: FOS: Biological sciences
subject: Genetics
subject: Biotechnology
subject: Ecology
subject: 69999 Biological Sciences not elsewhere classified
subject: Cancer

description: Additional file 1: Supplementary Materials and Methods. Table S1. MetaSIPSim dependencies. Table S2. Parameters used for the MetaSIPSim validation and case study simulations. * Values may differ between simulations as described in the materials and methods. Table S3. Processing times for all simulations from the cases study. All times are in seconds. Table S4. Summary statistics for recovery of reads, contigs, and MAGs for labeled genomes in initial simulations. Figure S1. Visual description of variables defined in the manuscript and Table 2. Thick blue line indicates the position of a single DNA fragment during and after ultracentrifugation. Centrifugation setup shown here is based on a fixed angled rotor. Figure S2. Diagram of experimental design for case study simulations. Figure S3. RefSeq genomes G + C distribution with G + C bins rounded to nearest whole number (downloaded January 25, 2019). Figure S4. G + C distributions for the 500 genomes in each reference set. G + C bins are rounded to the nearest whole number. Vertical line indicates G + C skew of the set. Figure S5. Rank-abundance plots for each simulated sample or replicate community including the 12C-control (Con) and all five 13C-trials (T1-T5). Random genomes are only labeled in the 13C-labeled samples. Vertical grey lines indicate ranks of the 50 labeled genomes per treatment. Labeled genomes were selected such that mean ranks of the labeled genomes averaged across all samples were similar across the reference sets (lowGC, medGC, and highGC). Figure S6. Fold difference in raw read coverage for each labeled genome between the metagenomic-SIP and shotgun metagenomic libraries from the original simulations. Values above one indicate greater coverage in the metagenomic-SIP compared to the shotgun metagenomic libraries. Figure S7. Fold difference in proportion of each labeled genome recovered by reads between the metagenomic-SIP and shotgun metagenomic libraries from the original simulations. Values above one indicate greater recovery in the metagenomic-SIP compared to the shotgun metagenomic libraries. Figure S8. Fold difference in raw read coverage for each labeled genome between the metagenomic-SIP and shotgun metagenomic libraries from the follow-up simulations. Values above one indicate greater coverage in the metagenomic-SIP compared to the shotgun metagenomic libraries. Simulation with the lowGC reference set with varying number of labeled genomes per sample is in the top row while the simulation with the highGC reference set with different sequencing window BD ranges is in the bottom row. Figure S9. Fold difference in proportion of each labeled genome recovered by reads between the metagenomic-SIP and shotgun metagenomic libraries from the follow-up simulations. Values above one indicate greater recovery in the metagenomic-SIP compared to the shotgun metagenomic libraries. Simulation with the lowGC reference set with varying number of labeled genomes per sample is in the top row while the simulation with the highGC reference set with different sequencing window BD ranges is in the bottom row. Figure S10. Difference in proportion of each labeled genome recovered in co-assembled contigs between the metagenomic-SIP and shotgun metagenomic libraries from the original simulations. Values above zero indicate greater recovery in the metagenomic-SIP compared to the shotgun metagenomic contigs. Figure S11. Difference in NGA50 of each labeled genome covered by co-assembled contigs between the metagenomic-SIP and shotgun metagenomic libraries from the original simulations. Values above zero indicate greater NGA50 in the metagenomic-SIP compared to the shotgun metagenomic contigs. Only genomes with over 50% recovery in both SIP and shotgun metagenomes were used in this analysis. Figure S12. Difference in proportion of each labeled genome recovered in co-assembled contigs between the metagenomic-SIP and shotgun metagenomic libraries from the follow-up simulations. Values above zero indicate greater recovery in the metagenomic-SIP compared to the shotgun metagenomic contigs. Simulation with the lowGC reference set with varying number of labeled genomes per sample is in the top row while the simulation with the highGC reference set with different sequencing window BD ranges is in the bottom row. Figure S13. Difference in NGA50 of each labeled genome covered by co-assembled contigs between the metagenomic-SIP and shotgun metagenomic libraries from the original simulations. Values above zero indicate greater NGA50 in the metagenomic-SIP compared to the shotgun metagenomic contigs. Only genomes with over 50% recovery in both SIP and shotgun metagenomes were used in this analysis. Simulation with the lowGC reference set with varying number of labeled genomes per sample is in the top row while the simulation with the highGC reference set with different sequencing window BD ranges is in the bottom row. Figure S14. Difference in binning quality between the SIP-metagenomes and shotgun metagenomes with the initial simulations using multiple bins per labeled genome. A) Difference in proportion of each labeled genome recovered in bins. B) Difference in the cumulative contamination for each labeled genome bin set. Figure S15. Difference in proportion of each labeled genome recovered in a single most complete bin between the metagenomic-SIP and shotgun metagenomic libraries from the follow-up simulations. Values above zero indicate greater recovery in the metagenomic-SIP compared to the shotgun metagenomic bins. Simulation with the lowGC reference set with varying number of labeled genomes per sample is in the top row while the simulation with the highGC reference set with different sequencing window BD ranges is in the bottom row.