alfie 1.0

alignment free identification of edna

alfie: an alignment-free, kingdom level taxonomic classifier for DNA barcode data.

Alfie classifies sequences using a neural network which takes k-mer frequencies (default k = 4) as inputs and makes kingdom level classification predictions. At present, the program contains trained models for classification of cytochrome c oxidase I (COI) barcode sequences to the taxonomic level: kingdom. The program is effective at classifying sequences >200 base pairs in length, and no alignment information is needed.

Alfie can be deployed from the command line for rapid file-to-file classification of sequences. This is an effective means of separating contaminant sequences in a DNA metabarcoding or environmental DNA dataset from sequences of interest.

For increased control, alfie can also be deployed as a module from within Python. The alfie package also contains functions that can aid a user in the training and application of a custom alignment-free classifier, which allows the program to be applied to different DNA barcodes (or genes) or on different taxonomic levels.