This is a project which is currently making use of HPC facilities at Newcastle University. It is active.
For further information about this project, please contact:
The project will investigate the oral and gut microbiome in participants with and without periodontal disease and inflammatory bowel disease. In addition, the project will investigate the circulating inflammatory proteome and immune cell populations in the same participant cohorts.
Velvet, Celera, or Metasim are to combine fragmented sequence data.
BLAST or FastANI to identify genes from metagenomic reads.
MEGAHIT or FastANI to assess the diversity of microbial communities.
SAMtools or FastANI to organize metagenomic data into bins for analysis.
BLAST or FastANI to classifying microbial content from metagenomic reads.
FastANI or SAMtools to compare metagenomic data across different samples.
FastANI or SAMtools to map metagenomic reads to reference genomes.
FastANI or SAMtools to assess the quality of metagenomic data.