南極内陸域における雲と放射の研究

Supplementary Methods. (PDF 686 kb

How to blow up a massive star

Unweighted UniFrac distance between benign, hyperplasia, and endometrial cancer cohorts. (PDF 8 kb

Supplemental data for "The uncultured portion of the human microbiome is neutrally assembled"

Multiple sequence alignment in fasta format, and matching phylogeny in newick format, for recA genes of cultured and yet-to-be-cultured microbes found in the human gut microbiome

Files for validation of beta diversity using 16S rDNA regions V3 to V5

Synthetic mock datasets (100 replicates) used for validation of beta diversity across synthetic communities using 16S rDNA region V3 to V5. File also includes scripts and resulting raw data for the validation

Files for validation of beta diversity using 16S rDNA regions V6 to V9

Synthetic mock datasets (100 replicates) used for validation of beta diversity across synthetic communities using 16S rDNA region V6 to V9. File also includes scripts and resulting raw data for the validation

Files for taxonomy comparison

Synthetic mock dataset used for taxonomy assignment comparison, across multiple read lengths. File includes scripts used and raw validation data

Library comparison in a realistic sample.

<p>Mantel <i>r</i> statistic comparing the unweighted UniFrac matrices for different short-read 16S libraries against a full-length 16S library, based on a real paired-end libary sequenced from stool samples. The paired reads have a higher correlation to the full-length library than any of the other single read libraries.</p><p>Library comparison in a realistic sample.</p

Files for validation with realistic synthetic reads

Synthetic mock datasets used for validation based on a realistic human stool microbiome dataset. These are NOT real bacterial reads. Those reads are available as example data from the IM-TORNADO pipeline. File includes scripts and raw validation data

Taxonomy comparison.

<p>Comparison of accuracy from taxonomy calls using paired, read 1 (R1), read 2 (R2), and full length 16S rDNA. Analyses were carried out using the Ribosomal Database Project taxonomy classifier with the complete Greengenes database. Using Paired read analysis provides more accurate taxonomic classification than either R1 or R2 alone across all taxonomic levels. Full length 16S rDNA was used for comparison purposes.</p><p>Taxonomy comparison.</p

Files for taxonomy comparison using reads with errors

Synthetic mock datasets (100 replicates) used for validation of taxonomy using reads with errors and different length. File also includes scripts and resulting raw data for the validation