(ver. 0.2.2)
Amquery is a unified searchable database of amplicon libraries, designed for fast similarity search of 16S rRNA amplicon libraries against a large database. This tool allows users to compare hundreds of samples in a matter of minutes and to maintain databases with seamless and fast sample insertion and search.
Note: this package is under development.
Clone this repo to some directory and run pip install --process-dependency-links . inside.
To index the samples from fasta-formatted INPUT_FILE, type following commands (WARNING! This step may take a long time):
mkdir index && cd index && amq init
amq build INPUT_FILE
Amquery will use a square root of Jensen-Shannon divergence over k-mer abundandcy distributions of sample reads by default. If you want to use weighted UniFrac instead, you must also provide proper OTU table and phylogenetic tree. Read amq init --help for further information.
Use the amq list to list all the indexed samples, and amq stats to view a short summary about the index.
amq find -k NUMBER_OF_NEIGHORS SAMPLE_NAME
This project is licensed under the terms of the MIT license.