lcerdeira/minuur repository overview

⁠MINUUR - Microbial INsights Using Unmapped Reads

Doi for manuscript: https://doi.org/10.12688/wellcomeopenres.19155.1⁠

Please follow the tutorial in my Jupyter Book Available Here: https://aidanfoo96.github.io/MINUUR/⁠ for reproduction of my analysis or to apply in your host of interest :)

MINUUR is a snakemake pipeline I developed to extract non-host sequencing reads from mosquito whole genome sequencing data and utilise a range of metagenomic analyses to characterise potential host-associated microbes. Its application can be applied to other host-associated WGS data. MINUUR aims to leverage pre-existing WGS data to recover microbial information pertaining to host associated microbiomes.

MINUUR utilises:

• KRAKEN2: Classify taxa from unmapped read sequences
• KrakenTools: extract classified reads for downstream analysis
• BRACKEN: reestimate taxonomic abundance from KRAKEN2
• MetaPhlan3: Classify taxa using marker genes
• MEGAHIT: Metagenome assemblies using unmapped reads
• QUAST: Assembly statistics from MEGAHIT assemblies
• MetaBat2: Bin contiguous sequences from MEGAHIT
• CheckM: Assess bin quality from MetaBat2

⁠Installation of Snakemake

MINUUR is run using the workflow manager Snakemake⁠

Snakemake is best installed using the package manager Mamba⁠

Once Mamba is installed run

mamba create -c bioconda -c conda-forge --name snakemake snakemake

⁠Installation of MINUUR

Use git clone https://github.com/aidanfoo96/MINUUR/ and cd MINUUR/workflow. This is the reference point from which the pipeline will be run. See the JupyterBooks page for a full tutorial on establishing the configuration to run this pipeline.

⁠Update 09/05/2023:

• Added Github actions
• Dummy dataset now included in workflow/data, tutorial for running this is included in the JupyterBooks page. Use this to ensure the pipeline works on your machine.
• Added the option to run BUSCO to help assess eukaryotic contamination in MAGs

Any feedback or bugs please open an issue or contact: [email protected]⁠