This module provides functionalities for parsing and processing taxonomic data
from Kraken and Metabuli output files. It includes structures and functions
for handling taxonomic levels, counting reads, and extracting taxonomic identifiers.
This module provides functionalities for cleaning and processing FASTQ files
using various aligners and classifiers. It includes the core structures and
implementations for executing the cleaning pipeline with the Scrubby tool.
This module provides structures and implementations for Scrubby,
which is used for read cleaning or extraction using k-mer classifiers
and aligners. It is primarily meant for benchmarking host depletion for
clinical metagenomic diagnostic applications in conjunction with syndromic
reference panel simulations and reference index construction including for
human and microbial pangenome databases with Cipher.