High-resolution tracking of microbial colonization in Fecal Microbiota Transplantation experiments via metagenome-assembled genomes

This project contains anvi'o profiles and contigs databases that is used and/or referenced from the Lee STM and Khan SA, et al. study titled "High-resolution tracking of microbial colonization in Fecal Microbiota Transplantation experiments via metagenome-assembled genomes". The pre-print of this study is available via http://dx.doi.org/10.1101/090993.

To be able to work with the data files you will need anvi'o v2.1.0 to be installed on your system. For installation instructions, or to have access to a Docker image for anvi'o, please visit this URL: http://merenlab.org/software/anvio

Public data:

ANVIO-FMT-D-R01-R02-QUICK-VISUALIZATION.tar.gz: Data files for a quick visualization of the 97 MAGs and their distribution across the two FMT recipients. A run script in the archive explains how to use this data.

ANVIO-FMT-D-R01-R02-MERGED-PROFILE.tar.gz: The merged anvi'o profile for the entire data, which also contains a collection of 97 MAGs identified in the donor. The profile database contains no hierarchical clustering of contigs, however, individual MAGs can be displayed via the following notation since the collection 'MAGs' describe the organization of contigs in each MAG referenced from the dataset `ANVIO-FMT-D-R01-R02-QUICK-VISUALIZATION`, as well as from the paper: "anvi-refine -c CONTIGS.db -p PROFILE.db -C MAGs -b FMT-Donor_MAG_00054". All MAG names are in the supplementary tables in our paper.

ANVIO-FMT-D-R01-R02-MAGs-SUMMARY.tar.gz: A static HTML website that contains FASTA files for each MAG, and TAB-delimited matrices for coverage and detection values, and others. After unpacking, you can double-click the index.html file.