dRep is a python program for rapidly comparing large numbers of genomes. dRep can also "de-replicate" a genome set by identifying groups of highly similar genomes and choosing the best representative genome for each genome set.

References:

• Matthew R Olm et al.dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication The ISME Journal volume 11, pages2864–2868 (2017) Journal

• drep Github:Github

• drep can be run as:

  	dRep --help
  	

• Figures are located within the work directory under figures folder:

  	ls out/figures/
  	Clustering_scatterplots.pdf
  	Cluster_scoring.pdf
  	Primary_clustering_dendrogram.pdf
  	Secondary_clustering_dendrograms.pdf
  	Winning_genomes.pdf
  	

  

Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf]$ sinteractive --cpus-per-task=10 --mem=20G
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144]$ module load drep
[user@cn3144]$ mkdir /data/$USER/drep_test/
[user@cn3144]$ cd /data/$USER/drep_test/
[user@cn3144]$ cp -r ${DREP_TEST_DATA:-none}/* .
[user@cn3144]$ dRep --help
...::: dRep v3.2.2 :::...

  Matt Olm. MIT License. Banfield Lab, UC Berkeley. 2017 (last updated 2020)

  See https://drep.readthedocs.io/en/latest/index.html for documentation
  Choose one of the operations below for more detailed help.

  Example: dRep dereplicate -h

  Commands:
    compare            -> Compare and cluster a set of genomes
    dereplicate        -> De-replicate a set of genomes
    check_dependencies -> Check which dependencies are properly installed


[user@cn3144]$ dRep dereplicate out3 -g ./test/*fasta
***************************************************
    ..:: dRep dereplicate Step 1. Filter ::..
***************************************************

Will filter the genome list
2 genomes were input to dRep
Calculating genome info of genomes
100.00% of genomes passed length filtering
Running prodigal
Running checkM
GenomeInfo has no values over 1 for contamination- these should be 0-100, not 0-1!
100.00% of genomes passed checkM filtering
***************************************************
    ..:: dRep dereplicate Step 2. Cluster ::..
***************************************************

Running primary clustering
Running pair-wise MASH clustering
2 primary clusters made
Running secondary clustering
Running 2 ANImf comparisons- should take ~ 0.2 min
Step 4. Return output
***************************************************
    ..:: dRep dereplicate Step 3. Choose ::..
***************************************************

Loading work directory
GenomeInfo has no values over 1 for contamination- these should be 0-100, not 0-1!
***************************************************
    ..:: dRep dereplicate Step 4. Evaluate ::..
***************************************************

will provide warnings about clusters
0 warnings generated: saved to /spin1/home/linux/apptest1/out3/log/warnings.txt
will produce Widb (winner information db)
Winner database saved to /spin1/home/linux/apptest1/out3data_tables/Widb.csv
***************************************************
    ..:: dRep dereplicate Step 5. Analyze ::..
***************************************************

making plots 1, 2, 3, 4, 5, 6
Plotting primary dendrogram
Plotting secondary dendrograms
Plotting MDS plot
Plotting scatterplots
GenomeInfo has no values over 1 for contamination- these should be 0-100, not 0-1!
Plotting bin scorring plot
GenomeInfo has no values over 1 for contamination- these should be 0-100, not 0-1!
Plotting winning genomes plot...

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    ..:: dRep dereplicate finished ::..

Dereplicated genomes................. /spin1/home/linux/apptest1/out3/dereplicated_genomes/
Dereplicated genomes information..... /spin1/home/linux/apptest1/out3/data_tables/Widb.csv
Figures.............................. /spin1/home/linux/apptest1/out3/figures/
Warnings............................. /spin1/home/linux/apptest1/out3/log/warnings.txt

$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$

[user@cn3144]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch input file (e.g. drep.sh). For example:

#!/bin/bash

#SBATCH --job-name=drep_run
#SBATCH --time=2:00:00

#SBATCH --partition=norm
#SBATCH --nodes=1
#SBATCH --mem=20g
#SBATCH --cpus-per-task=4

cd /data/$USER/drep_test
module load drep
dRep dereplicate out2 -g ./test/*fasta 

Submit this job using the Slurm sbatch command.

sbatch drep.sh