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:
Nucleotide sequence processing, genome assemblies, sequence mapping, predictive modelling, machine learning
Metagenomic and targeted amplicon sequence processing using mostly MiniConda tools including:
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.
Viral detection with VirSorter2, DeepVirFinder and CheckV.
Viral enrichment analysis with ViromeQC.
Also includes predictive modelling with machine learning tools including Keras and TensorFlow