filter_classified_reads

Filter for reads from taxa of interest using Kraken2/Centrifuge classification results.

• Free software: Apache Software License 2.0
• Documentation: https://filter-classified-reads.readthedocs.io.

Features

• Filter for union of reads classified to taxa of interest Kraken2 and Centrifuge (by default filter for Viral reads (taxid=10239))
• Output unclassified reads along with reads from taxa of interest or exlude them with –exclude-unclassified
• seqtk for quickly filtering reads and pbgzip for parallel block Gzip compression of output reads (recommended that these dependencies are installed with Conda)

Usage

Paired-end reads with classification results by both Kraken2 and Centrifuge

Using test data in tests/data/:

You should see the following log information:

Credits

This package was created with Cookiecutter and the audreyr/cookiecutter-pypackage project template.