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:
Processing of raw microbial DNA and RNA sequencing data, proteomics and metabolomics data generated from preterm infant samples.
Metagenomic and targeted amplicon sequence processing using mostly MiniConda tools including:
Amplicon sequence processing with Qiime2, dada2, and kraken2.
Quality control with FastP, human read filtering with Hostile and bowtie2.
Bacterial taxonomic and functional profiling with the MetaPhlAn and HUMaNn tools within the BioBakery suite.
Metagenomic genome assembly with Megahit.
Read mapping with Samtools, Bamtools and bwa-mem.
Assembly QC with CheckM and MetaBat2.
Read annotation with Blast.