Matt Ralston

Matt Ralston

M.Sc. Bioinfo + 5 years industry exp. - - - Looking for a position in biosciences. I'm gifted at the command line or computer terminal, but I perform best on my feet, standups, cleaning, guitar with samples in the centrifuge, more in the water bath, data being processed on the computer while I sleep, and other assays to plan. Currently writing a DNA sequence graph algorithm and manuscript (for bioRxiv). I play math rock on my guitar, I have some open-source software on GitHub, I pay my bills in the DE-NJ-PA tri-state area near Delco, and I'm launching a DE-based LLC for Univ. of Delaware and local NGS sequencing projects.

kmerdb kmeans

Standardizing on int64 for counts, kmerdb provides access to two k-means methods in the Python ecosystem: scikit-learn, and biopython.

Using k-means on k-mer count matrices, say on the first and second principal component of the artificial metagenome may reveal groupings of interest and other spatial characteristics of use for adjacent and concurrent analysis on hierarchical structures of the species diagram. Of course, more value is gained on large (30-200+ species) metagenomes.

This subcommand of the Python Package Authority (PyPA) package kmerdb writes/reads Pandas DataFrames from STDIN/STDOUT, and produces matplotlib graphics alongside the k-means elbow diagram choices (if k is not provided), and choice of k and principal components to provide for k-means clustering and visualization.

kmerdb kmeans -k 4 kmer_count_matrix_after_PCA.12.tsv