dRep物种集去冗余

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 https://data.ace.uq.edu.au/public/CheckM_databases/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
-sa ANI聚类阈值，默认0.99

使用

dRep dereplicate output_dir/ \
-g /path/to/genomes/*.fasta \
-p 10 \
-comp 70 
-con 10 \
-sa 0.95

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