Assembly Kmer Clustering

Jamie McGowan, 2023

Tool to cluster and visualise contigs from a genome assembly using kmer frequencies

Dependencies

• python
  • biopython
  • tqdm
• r
  • ggplot2
  • umap

Installation

You can install the dependencies using the provided yaml file conda_env.yaml

git clone https://github.com/jamiemcg/assembly_kmer_composition
cd assembly_kmer_composition

conda env create -f conda_env.yaml
conda activate assembly_kmer_composition

Usage

Kmer counting

The python script kmer_composition.py counts kmers from sequences in FASTA format of a specified kmer length

python kmer_composition.py [assembly.fasta] [kmer_length] [output_file]

For example, to count the frequencies of kmers of length 4 and save them to a file called tet.tsv:

python kmer_composition.py assembly.fasta 4 tet.tsv

Plotting

The R script plot_umap_kmer_freq.r clusters the contigs based on UMAP dimensionality reduction of kmer frequencies and plots clustered contigs.

Rscript plot_umap_kmer_freq.r [kmer_count_file.tsv] [output_dir] [output_prefix]

For example:

Rscript plot_umap_kmer_freq.r tet.tsv . my_assembly

Will create a file my_assembly_UMAP.tsv with the UMAP coordinates and a plot my_assembly_UMAP.pdf visualising the clusters.

Example plots

For example, here is plot showing a contaminated tardigrade assembly (GCA_001455005.1 ASM145500v1) clustered based on 4-mers:

You could overlay such plots with the output from a taxonomic classifier, e.g. here is the same plot with contigs coloured by Tiara classifications

Interactive Version

.....