Nature Biotechnology: doi: /nbt Supplementary Figure 1. Detailed overview of the primer-free full-length SSU rrna library preparation.
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1 Supplementary Figure 1 Detailed overview of the primer-free full-length SSU rrna library preparation. Detailed overview of the primer-free full-length SSU rrna library preparation.
2 Supplementary Figure 2 Detailed overview of the primer-based full-length SSU rrna library preparation. Detailed overview of the primer-based full-length SSU rrna library preparation.
3 Supplementary Figure 3 rrna length distribution after adapter trimming. rrna length distribution after adapter trimming.
4 Supplementary Figure 4 Maximum-likelihood phylogenetic tree showing coverage of the domain Bacteria. Maximum-likelihood phylogenetic tree showing coverage of the domain Bacteria. The tree includes all bacterial OTUs clustered at 97% generated in this study, their closest match in the Silva SSU NR99 v. 128 database and the reference set from the recent Tree of Life article (Hug et al., 2016). Hypervariable regions were masked with a 40% positional conservation filter, giving 1392 alignment positions, and the tree calculated using FastTree v SSE3 (Price et al., 2010). Clade names and clustering are based on the position of reference sequences. *Indicates clades that do not include a genome or pure culture reference sequence being based on classification of reference sequences in the Silva v. 128 taxonomy. Reference sequences appear black whilst those generated in the current study are color coded based on their similarity to existing database sequences.
5 Supplementary Figure 5 Rarefaction curves for the different samples split based on kingdom. Rarefaction curves for the different samples split based on kingdom.
6 Supplementary Figure 6 Maximum-likelihood phylogenetic tree showing coverage of the domain Archaea. Maximum-likelihood phylogenetic tree showing coverage of the domain Archaea. The tree includes all archaeal OTUs clustered at 97% generated in this study, their closest match in the Silva SSU NR99 v. 128 database and the reference set from the recent Tree of Life article (Hug et al., 2016). Hypervariable regions were masked with a 40% positional conservation filter, giving 1257 alignment positions, and the tree calculated using FastTree v S SE3 (Price et al., 2010). Clade names and clustering are based on the position of reference sequences. *Indicates clades that do not include a genome or pure culture reference sequence being based on classification of reference sequences in the Silva v taxonomy. Reference sequences appear black whilst those generated in the current study are color coded based on their similarity to existing database sequences.
7 Supplementary Figure 7 Maximum-likelihood phylogenetic tree showing coverage of the domain Eukarya. Maximum-likelihood phylogenetic tree showing coverage of the domain Eukarya. The tree includes all eukaryotic OTUs clustered at 97% generated in this study, their closest match in the Silva SSU NR99 v. 128 database and the reference set from the recent Tree of Life article (Hug et al., 2016). Hypervariable regions were masked with a 40% positional conservation filter, giving 1548 alignment positions, and the tree calculated using FastTree v S SE3 (Price et al., 2010). Clade names and clustering are based on the position of reference sequences. Reference sequences appear black whilst those generated in the current study are color coded based on their similarity to existing database sequences.
8 Supplementary Figure 8 Error-correction of Oxford Nanopore MinION data using molecular tagging. Error-correction of Oxford Nanopore MinION data using molecular tagging. Error-rate of the individual error-corrected consensus sequences as a function of the number of reads used to generate the consensus sequence. 1 represents the raw 2D reads.
9
10 Supplementary Figure 9 Data processing overview. Data processing overview. An overview of the data processing steps, important data outputs and data types used for different analysis.
Title ghost-tree: creating hybrid-gene phylogenetic trees for diversity analyses
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 Title ghost-tree: creating hybrid-gene phylogenetic trees for diversity analyses
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