Lemonade Creek, Yellowstone National Park, USA - Microbial Community Analysis - Genome and Transcriptome Data

<p>Genome and Transcriptome data used for analysis of microbial community function over a diurnal cycle in Lemonade Creek, Yellowstone National Park, USA.</p> <p>&nbsp;</p> <p><code>mags.tar</code>&nbsp; Non-redundant metagenome data (genome assemblies, predicted genes, and gene functional annotations).</p> <p>&nbsp;</p> <p>In each directory are the the following files:</p> <p>- <code>*.mRNA.faa</code> protein sequences of protein-coding genes</p> <p>- <code>*.mRNA.fna</code> nucleotide sequences of protein-coding genes</p> <p>- <code>*.mRNA.gff3</code> genomic location of protein-coding genes</p> <p>- <code>*.mRNA.emapper.tsv</code> eggNOG-mapper annotations for the protein-coding genes</p> <p>- <code>*.mRNA.interproscan.gff3</code> InterProScan annotations for the protein-coding genes</p> <p>&nbsp;</p> <p>In the <code>prokaryote</code> directory there are the following files:</p> <p>- <code>*.rRNA.fna</code> nucleotide sequences of rRNA genes</p> <p>- <code>*.rRNA.gff3</code> genomic location of rRNA genes</p> <p>- <code>*.tRNA.fna</code> nucleotide sequences of tRNA genes</p> <p>- <code>*.tRNA.gff3</code> genomic location of tRNA genes</p> <p>- <code>*.other.fna</code> nucleotide sequences of other genes (i.e., CRISPR, ncRNA, oriC, regulatory_region, repeat_region, tmRNA - if any were predicted)</p> <p>- <code>*.other.gff3</code> genomic location of other genes</p> <p>&nbsp;</p> <p><strong>Eukaryotes</strong></p> <p>Five MAGs from other eukaryotes that were assembled from a coassembly of the Soil samples.</p> <p>&nbsp;</p> <p><strong>Prokaryotes</strong></p> <p>The final dereplicated prokaryote MAGs (at 95% ID). The two&nbsp;<code>*stats*</code> files list the taxonomic information (from <code>GTDB-Tk</code>), completeness (from <code>CheckM</code>), and assembly stats (from the <code>stats.sh</code> script from the <code>bbmap</code> package) for each of the prokaryotic MAGs + the number of predicted protein-coding and non-protein-coding genes predicted in each MAG.</p> <p>&nbsp;</p> <p><strong>Viruses</strong></p> <p>The final dereplicated viral MAGs and vOTUs.</p> <p>&nbsp;</p> <p>&nbsp;</p> <p>&nbsp;</p> <p><code>read_mapping.tar</code> Abundance results from metagenome and metatranscriptome read mapping analysis against the non-redundant metagenome data and predicted genes (respectively). This analysis includes the&nbsp;cyanidiophyceae reference nuclear and organelle genomes.</p> <p>&nbsp;</p> <p><strong>mags</strong></p> <p>Results from <code>bbmaps</code> alignment of metagenome reads against a database of non-redudant metagenome MAGs + cyanidiophyceae reference nuclear and organelle genomes. <code>CoverM</code> was used to calculate MAG abundances.</p> <p>&nbsp;</p> <p><strong>genes</strong></p> <p><code>Salmon</code> abundance quantification of PolyA and RiboMinus metatranscriptome reads mapped against the predicted genes in the non-redudant metagenome MAGs + cyanidiophyceae reference nuclear and organelle genomes.</p>