## McMahon Lab Freshwater Lakes Database This repository is a private database for members of the McMahon Lab to store and share temporary drafts of metagenome-assembled genomes (MAGs) from freshwater lake metagenomic projects that are not ready to be made publicly available. Currently the database contains the following folders: - ref_MAGs_historical - Mendota - TroutBog_epi - TroutBog_hypo - Mary - CrystalBog - GEODES The only set of MAGs that are currently publicly available are the ref_MAGs_historical bins. These are available on the JGI IMG database and the [public Freshwater_Microbial_Observatory repository](https://osf.io/5syhe/). This public repository also contains assembled contigs from each sequenced metagenome from Lake Mendota, Trout Bog epilimnion, and Trout Bog hypolimnion. This public facing repository serves as the landing place where temporary drafts of MAGs will be published with their corresponding analyses after they are further refined. Within each folder contains the following files corresponding to genomes assembled from that lake: - All dereplicated bins assembled from the lake in fasta format (.fa) in a compressed tarball - A metadata file describing for each MAG the taxonomical classification and quality statistics - Mapping statistics for each bin for each metagenomic sample, denoted by date. **Note that mapping statistics will likely need to be redone for any set of MAGs as further refinement and quality checks are applied. These are meant to provide rough estimates so users can explore lineages of interest** The GEODES folder is a slight modification of this format, as within this folder it is then split into sub-folders by lake. The GEODES project was a paired metagenomic and metatranscriptomic investigation of diel cycles by Alex Linz. Therefore, these assembled genomes are for using specifically with the metagenomes sequenced during this experiment and the corresponding 48-hour metatranscriptomic experiments. For each lake folder in the GEODES folder, there are the following folders: - All dereplicated bins assembled from that lake in fasta format (.fa) in a compressed tarball - A metadata file describing for each MAG the taxonomical classification and quality statistics - A metagenomic and metatranscriptomic mapping statistics file. For each bin, the stats for metagenomic reads mapping back to each bin for the two samples and metatranscriptomic reads mapping back to each bin over the 48-hour period. Within this wiki contain pages on how metagenomic assembly and binning was performed to obtain these sets of bins, parameters for preliminary metagenomic and metatranscriptomic mapping, and suggestions for best practices for further refining bins.