This repository contains resources related to the manuscript describing the MetaGraph framework, such as supplemental data tables containing sample metadata, example scripts and interactive notebooks. Please find below a more detailed description of each category under the respective section.
Disclaimer: This repository is currently still under construction and more content will be added within the next days. Some of the sections are still incomplete.
All metadata tables of sample cohorts analyzed in the manuscript can be found in the data_tables directory. Please note that the data items in this repository utilize the git-lfs framework. You need to install git-lfs on your system to be able to download and access the data. The following table summarizes, which table relates to which cohort.
| Dataset Description | File |
|---|---|
| Sample metadata for the SRA-Microbe index | data_tables/TableS1_SRA_Microbe.tsv.gz |
| Sample metadata for the SRA-Fungi index | data_tables/TableS2_SRA_Fungi.tsv.gz |
| Sample metadata for the SRA-Plant index | data_tables/TableS3_SRA_Plant.tsv.gz |
| Sample metadata for the SRA-Metazoa index | data_tables/TableS4_SRA_Metazoa.tsv.gz |
| Sample metadata for the SRA-MetaGut index | data_tables/TableS5_SRA_MetaGut.tsv.gz |
| Sample metadata for the MetaSUB index | data_tables/TableS6_MetaSUB.csv.gz |
| Sample metadata for the GTEx index | data_tables/TableS7_GTEX.txt |
| Sample metadata for the TCGA index | data_tables/TableS8_TCGA.tsv.gz |
| List of E. coli reference genomes used for accuracy experiment | data_tables/TableS9_EColi.txt |
| Sample metadata for the SRA-Microbe index which was extracted from McCortex logs | data_tables/TableS10_SRA_Microbe_McCortex_logs.tsv.gz |
| List of SRA IDs in SRA-Microbe with no available metadata | data_tables/TableS11_SRA_Microbe_no_logs.tsv |
| Sample metadata for the SRA-Public (100 studies) index | data_tables/TableS12_SRA_Public_100studies.tsv.gz |
| Hosting cost calculations for MetaGraph indexes | data_tables/TableS15_Hosting_Costs.xlsx |
This folder contains Ipython notebooks that can be used as examples to show how to interact with the graph indexes served on local or remote servers. Some of the result panels presented in the MetaGraph manuscript can be reproduced using these notebooks.
This folder contains the scripts used to run the experiments presented in the MetaGraph manuscript.