Skip to main content

alignment free identification of edna

Project description

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.

Project details


Release history Release notifications | RSS feed

This version

1.0

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Files for alfie, version 1.0
Filename, size File type Python version Upload date Hashes
Filename, size alfie-1.0-py3-none-any.whl (40.3 MB) File type Wheel Python version py3 Upload date Hashes View
Filename, size alfie-1.0.tar.gz (40.2 MB) File type Source Python version None Upload date Hashes View

Supported by

AWS AWS Cloud computing Datadog Datadog Monitoring DigiCert DigiCert EV certificate Facebook / Instagram Facebook / Instagram PSF Sponsor Fastly Fastly CDN Google Google Object Storage and Download Analytics Microsoft Microsoft PSF Sponsor Pingdom Pingdom Monitoring Salesforce Salesforce PSF Sponsor Sentry Sentry Error logging StatusPage StatusPage Status page