Single-Cell Analysis of Host-Microbiome Interactions
Barcode level signal denoising
Extract reads and output from Kraken
Parse kraken report file
Prepare kraken report, k-mer statistics, UMI data
Identifying contaminants and false positives taxa (cell line quantile ...
Sample level signal denoising
Quantitation of microbes
A computational resource designed to accurately detect microbial nucleic acids while filtering out contaminants and false-positive taxonomic assignments from standard transcriptomic sequencing of mammalian tissues. For more details, see Ghaddar (2023) <doi:10.1038/s43588-023-00507-1>. This implementation leverages the 'polars' package for fast and systematic microbial signal recovery and denoising from host tissue genomic sequencing.