生物信息怎么算出来的？——微生物基因组评估用到的完整度、污染度计算算法

 I 知识背景

CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes. It provides robust estimates of genome completeness and contamination by using collocated sets of genes that are ubiquitous and single-copy within a phylogenetic lineage. Assessment of genome quality can also be examined using plots depicting key genomic characteristics (e.g., GC, coding density) which highlight sequences outside the expected distributions of a typical genome. CheckM also provides tools for identifying genome bins that are likely candidates for merging based on marker set compatibility, similarity in genomic characteristics, and proximity within a reference genome tree.

II 计算原理

Estimation of completeness, contamination, and strain heterogeneity

 III 安装流程：

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#1.通过conda安装
conda create -n checkm
conda activate checkm
conda install -c bioconda checkm-genome
#2.通过pip安装
pip3 install numpy
pip3 install matplotlib
pip3 install pysam
pip3 install checkm-genome
conda install hmmer prodigal pplacer
#3.下载数据库并设置数据路径
wget -c https://data.ace.uq.edu.au/public/CheckM_databases/checkm_data_2015_01_16.tar.gz
tar -zxvf checkm_data_2015_01_16.tar.gz
checkm data setRoot /path/to/checkm_data
#4.安装成功后，测试通过命令
checkm lineage_wf -t 150 -x fasta -f sag_2554.txt --tab_table ../fasta_file output

四、参考文献
https://ecogenomics.github.io/CheckM/
Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. 2014. Assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Research, 25: 1043-1055.