KMCP Manuscript Data

# KMCP: accurate metagenomic profiling of both prokaryotic and viral populations by pseudo-mapping

## 1.code-and-documents

This directory contains the source code, executable binaries, and documents of KMCP,
which are also hosted at Github: https://github.com/shenwei356/kmcp .

Databases, usage, and tutorials of KMCP are also available at https://bioinf.shenwei.me/kmcp/.

- [Installation](https://bioinf.shenwei.me/kmcp/download)
- [Databases](https://bioinf.shenwei.me/kmcp/database)
- Tutorials
    - [Taxonomic profiling](https://bioinf.shenwei.me/kmcp/tutorial/profiling)
    - [Sequence and genome searching](https://bioinf.shenwei.me/kmcp/tutorial/searching)
- [Usage](https://bioinf.shenwei.me/kmcp/usage)
- [Benchmarks](https://bioinf.shenwei.me/kmcp/benchmark)
- [FAQs](https://bioinf.shenwei.me/kmcp/faq)

## 2.databases

This directory contains the building steps and reference genome accessions for
KMCP databases used in the manuscript.

    cami2     Databases used in benchmarks on CAMI2 mouse gut datasets
    kmcp      Databases used in other benchmarks
    
## 3.figures

Each subdirectory contains steps to run the benchmark (`README.md`), steps for plotting (`README-plot.md`),
benchmark results, and figures.