We implemented a K-mer search for DNA sequences and analyzed its effectiveness comparing to a full alignment search in identifying microbiome DNA strands in Pittsburgh rivers.
Water samples were collected at six different locations (including pure water as control). DNAs were extracted and sequenced beforehand in the wet-lab.
The sequence reads are available in data/Fall2018CleanReads.fa. DNA reads quality control data and reports are available in dna_quality_control/.
We also used bacterial_16s_genes.fa, which contains bacterial 16s genes as the database that we search against.
Simply run microbiome_test.py and bacterial phylum plots will be generated in the fraction_plots/ directory with our pre-tuned parameters (K=8, thresh=.6 -> Acc 0.973) for k-mer search (see details here).
An analysis report on parameter search has been provided in kmer_size_acc_reports/ with accuracy data included.
We have run a full alignment (consult alignment.py for its implementation details) on the DNA reads against the s16 database on Google Cloud and the result is saved in data/*.txt. Runtime generated calculations have been saved in cache/*.pickle. You may perform further analysis on these.
Anupam Pokharel and Dr. Kangas