parse_kraken_report

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.

Yun Peng

rsahmi

Single-Cell Analysis of Host-Microbiome Interactions

parse_kraken_report function

<dl><dt>kraken_report</dt>
<dd>The path to kraken report file.</dd>
<dt>intermediate_ranks</dt>
<dd>A bool indicates whether to include
non-traditional taxonomic ranks in output.</dd>
<dt>mpa</dt>
<dd>A bool indicates whether to use mpa-style.</dd></dl>

Arguments

Parse kraken report file — parse_kraken_report

<dl>

<dt>kraken_report</dt>
<dd>The path to kraken report file.</dd>


<dt>intermediate_ranks</dt>
<dd>A bool indicates whether to include
non-traditional taxonomic ranks in output.</dd>


<dt>mpa</dt>
<dd>A bool indicates whether to use mpa-style.</dd>

</dl>

parse_kraken_report: Parse kraken report file

Description

Usage

Value

Arguments

See Also