Traing Data for "Assembly of metagenomic sequencing data" tutorial

<p>Metagenomics involves the extraction, sequencing and analysis of combined genomic DNA from <strong>entire microbiome</strong> samples. It includes then DNA from <strong>many different organisms</strong>, with different taxonomic background.</p> <p>Reconstructing the genomes of microorganisms in the sampled communities is critical step in analyzing metagenomic data. To do that, we can use <strong>assembly</strong> and assemblers, <em>i.e.</em> computational programs that stich together the small fragments of sequenced DNA produced by sequencing instruments.</p> <p>Assembling seems intuitively similar to putting together a jigsaw puzzle. Essentially, it looks for reads &ldquo;that work together&rdquo; or more precisely, reads that overlap. Tasks like this are <strong>not straightforward</strong>, but rather complex because of the complexity of the genomics (specially the repeats), the missing pieces and the errors introduced during sequencing.</p> <p>In this tutorial, we will learn how to run metagenomic assembly tool and evaluate the quality of the generated assemblies. To do that, we will use data from the study: <a href="https://www.ebi.ac.uk/metagenomics/studies/MGYS00005630#overview">Temporal shotgun metagenomic dissection of the coffee fermentation ecosystem</a>. For an in-depth analysis of the structure and functions of the coffee microbiome, a temporal shotgun metagenomic study (six time points) was performed. The six samples have been sequenced with Illumina MiSeq utilizing whole genome sequencing.</p> <p>Based on the 6 original dataset of the coffee fermentation system, we generated mock datasets for this tutorial.</p>