Reproducible scripts for the manuscript Fast, lightweight, and accurate metagenomic functional profiling using FracMinHash sketches. The associated preprint will be added soon.
- Environment setup
- Part 1: comparison with other tools
- Part 2: analyze HMP functional profiles
- Part 3: functional UniFrac
git clone https://github.com/KoslickiLab/KEGG_sketching_annotation_reproducibles.git
cd KEGG_sketching_annotation_reproducibles
conda create -y --name annotate_ko
conda activate annotate_ko
conda install -y -c conda-forge -c bioconda --file ./src/requirements.txt
The manuscript comprises three distinct experimental sections, with each section encompassing multiple subtasks. It's not necessary to do one after the other. Under the same conda environment, please refer to each specific section below to reproduce the corresponding results.
This segment replicates the findings presented in Section 3.1, where benchmarking analyses of sourmash were conducted in comparison to other tools.
Please follow this guideline to reproduce all results (link below):
https://github.com/KoslickiLab/KEGG_sketching_annotation_reproducibles/blob/main/part1_comparison_with_other_tools/README.md
This segment replicates the findings presented in Section 3.2, where we utilized sourmash to get functional profiles of all HMP gut microbiome data and further analyzed the outputs.
Please follow this guideline to reproduce all results (link below):
https://github.com/KoslickiLab/KEGG_sketching_annotation_reproducibles/blob/main/part2_analyze_HMP_data/README.md