| Summary: | This data archive contains results generated using a high resolution shotgun metagenomics (HRSM) bioinformatic pipeline (ShotgunMG - https://jtremblay.github.io/shotgunmg.html) for the following projects: Human gut microbiome dataset: PRJNA588513 Antarctic soil dataset: PRJNA513362 Agricultural soil dataset: PRJNA513362 Mock communities: PRJNA873699 These analyses were performed in the context of evaluating if shallow shotgun metagenomic sequencing is an adequate approach to analyze SM sequencing data using a HRSM pipeline. Briefly, these PRJNA projects were analyzed using identical bioinformatic procedures, but using various initial raw sequencing data loads. Notable end results in each archive includes: de novo co-assembly (fasta files), contigs and genes abubance matrices. Beta-diversity (Bray-Curtis dissimilarity matrices), alpha diversity (richness, chao1, Simpson and Shannon indexes matrices), taxonomic summaries from the kingdom to up to the species level and Metagenome Assembled Genomes (MAGs). This dataset is link to the scientific manuscript entitled: High resolution shotgun metagenomics: the more data, the better? commands.tar.gz : contains all commands for a complete analysis of a given workflow type. Includes software versioning. export_antarctic_microbiome.tar.gz : contains all key results of every workflow related to the antarctic dataset. export_human_gut_microbiome.tar.gz : contains all key results of every workflow related to the human dataset.
|
|---|