drep可对基因组集去冗余，留下非冗余基因组集。从运行过程来看，先进行基因预测，然后用chekm做基因组质控，也因此需要安装配置checkm，去冗余基于ANI有关的参数。
文献信息
标题：dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication
期刊：ISME J
时间：2017
文档
drep：https://drep.readthedocs.io/en/latest/overview.html
checkm：https://github.com/Ecogenomics/CheckM/wiki
checkm_db: https://data.ace.uq.edu.au/public/CheckM_databases/
安装
# drep
conda install -c bioconda drep
# checkm
conda install hmmer pplacer
pip3 install checkm-genome
# checkm 数据库
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
export CHECKM_DATA_PATH=/path/to/my_checkm_data
帮助文档
dRep --help
# Commands:
# compare -> Compare and cluster a set of genomes
# dereplicate -> De-replicate a set of genomes
# check_dependencies -> Check which dependencies are properly installed
dRep dereplicate --help
-g 基因组集
-p 线程数
-comp 最小基因组完整度，默认75
-con 最大基因组污染度，默认25
-pa ANI threshold to form primary (MASH) clusters (default: 0.9)
-sa ANI threshold to form secondary clusters (default: 0.95)
--SkipSecondary Skip secondary clustering, just perform MASH clustering (default: False)
-l 长度筛选，默认50000
--ignoreGenomeQuality 忽略质量检测
使用
dRep dereplicate output_dir/ \
-g /path/to/genomes/*.fasta \
-p 10 \
-comp 70
-con 10 \
-sa 0.95 --SkipSecondary
过程
***************************************************
..:: dRep dereplicate Step 1. Filter ::..
***************************************************
Will filter the genome list
2,295 genomes were input to dRep
Calculating genome info of genomes
100.00% of genomes passed length filtering
Running prodigal
Running checkM
Running checkM in 2 chunks
Running checkM chunk 0
Running checkM chunk 1
21.83% of genomes passed checkM filtering
***************************************************
..:: dRep dereplicate Step 2. Cluster ::..
***************************************************
Running primary clustering
Running pair-wise MASH clustering
117 primary clusters made
Running secondary clustering
Running 3611 ANImf comparisons- should take ~ 45.1 min
Step 4. Return output
***************************************************
..:: dRep dereplicate Step 3. Choose ::..
***************************************************
Loading work directory
***************************************************
..:: dRep dereplicate Step 4. Evaluate ::..
***************************************************
etc
***************************************************
..:: dRep dereplicate Step 5. Analyze ::..
***************************************************
making plots 1, 2, 3, 4, 5, 6
Plotting primary dendrogram
Plotting secondary dendrograms
Plotting MDS plot
Plotting scatterplots
Plotting bin scorring plot
Plotting winning genomes plot...
$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$
..:: dRep dereplicate finished ::..
Dereplicated genomes................. 02_bin/bins_drep/dereplicated_genomes/
Dereplicated genomes information..... 02_bin/bins_drep/data_tables/Widb.csv
Figures.............................. 02_bin/bins_drep/figures/
Warnings............................. 02_bin/bins_drep/log/warnings.txt
/bins_drep_comp70/data_tables
Bdb.csv 基因组长度
Cdb.csv 聚类信息
Chdb.csv 基因组详细信息
genomeInformation.csv 完成度污染度
Mdb.csv 基因组两两距离
## 聚类信息
cat Cdb.csv | awk -F"," 'BEGIN{OFS="\t"}{print $1,$2,$6}' > cluster.info
# 代表基因组规则
LFY_1_1.12.fa 82_0 82
LFY_1_1.18.fa 11_1 11
LFY_1_4.17.fa 106_1 106
LFY_1_4.26.fa 110_1 110
LFY_1_4.2.fa 116_1 116
# 每个cluster基因组数量
cat cluster.info | sed '1d' | awk '{print $2}' | sort | uniq -c | sort -k 1nr > cluster.count
案例-推荐
pa primary threshold，不进行二次聚类，代表序列数=cluster数
dRep dereplicate 02_plasmid/01_drep \
-g 02_plasmid/00_plasmid/*.fa \
-p 16 -l 1 \
-pa 0.95 --ignoreGenomeQuality --SkipSecondary
checkm单独使用
checkm data setRoot $PATH/checkm_data
checkm lineage_wf \
-t 30 -x fa --nt --tab_table \
-f checkm_out.txt bins_samples checkm_out
更多：
CheckM：基因组质量评估
