Deep metagenome sequencing of the bovine gastrointestinal tract with multiple libraries

To obtain highly contiguous metagenome-assembled genomes (MAGs) of the microbiome in the bovine gastrointestinal tract (GIT), we generated multiple libraries consisting of paired-ends, mate-pairs, and linked reads (barcoded reads) for each GIT region of a single individual. The targeted GIT regions covered rumen, reticulum, omasum, abomasum, small intestine, and large intestine. We also generated metagenome shotgun paired-ends and 16S-amplicon reads of other individuals for downstream analysis.