Category Jekyll
UV: A Fast Package Manager for Python
As a bioinformatician, you likely use Python packages like BioPython, scanpy, or scikit-bio. Installing and managing these packages has traditionally been done with pip or conda, but these tools can...
Compositional Data Analysis for Microbiome Studies
Microbiome data is inherently compositional - the counts we obtain from sequencing provide information about the relative abundance of taxa, not their absolute abundance in the original sample. This has...
Using Micromamba
Micromamba is a fast, lightweight version of the Mamba package manager. Unlike Miniconda, it comes as a single executable with no default Python installation or base environment, making it perfect...
Category tutorial
Removing custom hosts from metagenomics
Hostile is a fantastic tool for removing host reads from whole metagenome shotgun datasets. It’s very user-friendly and has pre-built databases for human and murine reads decontaminating.
UV: A Fast Package Manager for Python
As a bioinformatician, you likely use Python packages like BioPython, scanpy, or scikit-bio. Installing and managing these packages has traditionally been done with pip or conda, but these tools can...
Compositional Data Analysis for Microbiome Studies
Microbiome data is inherently compositional - the counts we obtain from sequencing provide information about the relative abundance of taxa, not their absolute abundance in the original sample. This has...
Bioinformatics tutorials
Each markdown file will not have any “header1” section: the title of the page is defined in the header by the title: tag.
Bioinformatics tutorials
The bioinformaticians of the Core Bioinformatics team at the Quadram Institute Bioscience curates this blog with tutorials and hands-out for microbial genomics training.
Using Micromamba
Micromamba is a fast, lightweight version of the Mamba package manager. Unlike Miniconda, it comes as a single executable with no default Python installation or base environment, making it perfect...
Category metagenomics