MetaBench

MetaBench is a pipeline to continuously benchmark metagenomics analysis tools. It covers database construction (build), taxonomic binning and profiling.

It supports:

multiple tools
- in several release versions
multiple databases
- multiple range of parameters
multiple samples
- for binning and profiling both with multiple range of parameters
multiple evaluation metrics and threshold
performance benchmarks with optional repeats

It outputs:

standardized JSON files for integration
bioboxes output files for binning and profiling
interactive dashboard to analyze results

It requires:

Reference sequences to build databases
Set of reads in fastq and ground truth in the bioboxes format

Current configured tools:

ganon v2.0.0
kmcp v0.9.4
metacache v2.3.1
kraken2 v2.1.3
bracken v2.9

Installation and requirements

MetaBench is written in Snakemake and makes use of conda/mamba internally to install dependencies. It uses Bokeh to plot the interactive dashboard.

mamba create -n metabench_env snakemake genome_updater pandas "bokeh==2.4.3"
source activate metabench_env
pip install randomname
git clone https://github.com/pirovc/metabench.git
cd metabench

Usage example

Build

Downloading a small reference set for the build with genome_updater:

genome_updater.sh -d refseq -g bacteria -c "reference genome" -f "genomic.fna.gz" -o example/bac_rs -b refgen -t 8 -a

Create config/build_test.yaml:

workdir: "example/build/"
threads: 8
repeat: 1

tools:
  ganon:
    "2.0.0": ""
  kmcp:
    "0.9.4": ""

dbs:
  "bac_rs_refgen":
    folder: "../bac_rs/refgen/files/"
    extension: ".fna.gz"
    taxonomy: "ncbi"
    taxonomy_files: "../bac_rs/refgen/taxdump.tar.gz"
    assembly_summary: "../bac_rs/refgen/assembly_summary.txt"

run:
   ganon:
     "2.0.0":
       bac_rs_refgen:
         fixed_args:
           "--ncbi-file-info": "../bac_rs/refgen/assembly_summary.txt"
         args:
           "--max-fp": [0.0001, ""]
   kmcp:
     "0.9.4":
       bac_rs_refgen:
         fixed_args:
         args:

In the example above MetaBench is set to build databases for 2 tools (ganon and kmcp). kmcp will run with default parameters only (no args:) and ganon will run with --max-fp 0.0001 and default parameters.

Verify run with --dry-run:

snakemake -s metabench/build.smk --configfile config/build_test.yaml --cores 8 --use-conda --dry-run

Run it:

snakemake -s metabench/build.smk --configfile config/build_test.yaml --cores 8 --use-conda

If everything finished correctly, the following files will be created:

Files

$ tree -A example/build/

example/build/
├── ganon
│   └── 2.0.0
│       └── bac_rs_refgen
│           ├── default
│           │   ├── ganon_db.hibf
│           │   ├── ganon_db.ibf -> ganon_db.hibf
│           │   └── ganon_db.tax
│           ├── default.build.bench.json
│           ├── default.build.bench.tsv
│           ├── default.build.log
│           ├── default.build.size.tsv
│           ├── --max-fp=0.0001
│           │   ├── ganon_db.hibf
│           │   ├── ganon_db.ibf -> ganon_db.hibf
│           │   └── ganon_db.tax
│           ├── --max-fp=0.0001.build.bench.json
│           ├── --max-fp=0.0001.build.bench.tsv
│           ├── --max-fp=0.0001.build.log
│           └── --max-fp=0.0001.build.size.tsv
└── kmcp
    └── 0.9.4
        └── bac_rs_refgen
            ├── default
            │   └── kmcp_db
            │       ├── name.map
            │       ├── R001
            │       │   ├── _block001.uniki
            │       │   ├── _block002.uniki
            │       │   ├── __db.yml
            │       │   └── __name_mapping.tsv
            │       ├── taxid.map
            │       └── taxonomy
            │           ├── citations.dmp
            │           ├── delnodes.dmp
            │           ├── division.dmp
            │           ├── gc.prt
            │           ├── gencode.dmp
            │           ├── images.dmp
            │           ├── merged.dmp
            │           ├── names.dmp
            │           ├── nodes.dmp
            │           └── readme.txt
            ├── default.build.bench.json
            ├── default.build.bench.tsv
            ├── default.build.log
            └── default.build.size.tsv

*.build.bench.json contains the standardized metrics in JSON format. If repeat > 1 in the config file, only the fastest run is selected.
*.build.bench.tsv contains the raw benchmark metrics from Snakemake. If repeat > 1 in the config file, one line for each run will be reported.
*.build.log contains the STDOUT and STDERR from the run.
*.build.size.tsv contains the size in bytes for the mandatory database files (du --bytes).

Obs: note that if no arguments are used in args: section of the configuration, the database folder/files will be named default. If parameters are used, databases are created based on them (--max-fp 0.0001 -> --max-fp=0.0001, if more than one, connected by underscore "_"). Any information provided in fixed_args: is not accounted for file/folder names.

Check the config/build_example.yaml for more examples on how to use the configuration file. Multiple databases, range of parameters and others can be configured to be executed in the same run.

Classify (binning profiling)

Classification includes both binning and profiling procedures. It requires databases (as created in the build process above) and one or more samples with single or paired fastq files.

Create config/classify_test.yaml:

workdir: "example/classify/"
threads: 8
repeat: 1

tools:
  ganon:
    "2.0.0": ""
  kmcp:
    "0.9.4": ""

samples:
  "mende.10species.10K":
    fq1: "../../files/illumina_10species.10K.1.fq.gz"
    fq2: "../../files/illumina_10species.10K.2.fq.gz"

run:
  ganon:
    "2.0.0":
      dbs: 
        "bac_rs_refgen": "../../example/build/ganon/2.0.0/bac_rs_refgen/"
      fixed_args:
      binning_args:
        "--rel-cutoff": [0.25, 0.8]
      profiling_args:

  kmcp:
    "0.9.4":
      dbs: 
        "bac_rs_refgen": "../../example/build/kmcp/0.9.4/bac_rs_refgen/"
      fixed_args:
      binning_args:
      profiling_args:

Verify run with --dry-run:

snakemake -s metabench/classify.smk --configfile config/classify_test.yaml --cores 8 --use-conda --dry-run

Run it:

snakemake -s metabench/classify.smk --configfile config/classify_test.yaml --cores 8 --use-conda

If everything finished correctly, the following files will be created:

Files

$ tree -A example/classify/

example/classify/
├── ganon
│   └── 2.0.0
│       └── mende.10species.10K
│           └── bac_rs_refgen
│               ├── default
│               │   ├── --rel-cutoff=0.25
│               │   │   ├── default.profiling.bench.json
│               │   │   ├── default.profiling.bench.tsv
│               │   │   ├── default.profiling.bioboxes.gz
│               │   │   └── default.profiling.log
│               │   ├── --rel-cutoff=0.25.binning.bench.json
│               │   ├── --rel-cutoff=0.25.binning.bench.tsv
│               │   ├── --rel-cutoff=0.25.binning.bioboxes.gz
│               │   ├── --rel-cutoff=0.25.binning.log
│               │   ├── --rel-cutoff=0.25.rep
│               │   ├── --rel-cutoff=0.8
│               │   │   ├── default.profiling.bench.json
│               │   │   ├── default.profiling.bench.tsv
│               │   │   ├── default.profiling.bioboxes.gz
│               │   │   └── default.profiling.log
│               │   ├── --rel-cutoff=0.8.binning.bench.json
│               │   ├── --rel-cutoff=0.8.binning.bench.tsv
│               │   ├── --rel-cutoff=0.8.binning.bioboxes.gz
│               │   ├── --rel-cutoff=0.8.binning.log
│               │   └── --rel-cutoff=0.8.rep
│               └── --max-fp=0.0001
│                   ├── --rel-cutoff=0.25
│                   │   ├── default.profiling.bench.json
│                   │   ├── default.profiling.bench.tsv
│                   │   ├── default.profiling.bioboxes.gz
│                   │   └── default.profiling.log
│                   ├── --rel-cutoff=0.25.binning.bench.json
│                   ├── --rel-cutoff=0.25.binning.bench.tsv
│                   ├── --rel-cutoff=0.25.binning.bioboxes.gz
│                   ├── --rel-cutoff=0.25.binning.log
│                   ├── --rel-cutoff=0.25.rep
│                   ├── --rel-cutoff=0.8
│                   │   ├── default.profiling.bench.json
│                   │   ├── default.profiling.bench.tsv
│                   │   ├── default.profiling.bioboxes.gz
│                   │   └── default.profiling.log
│                   ├── --rel-cutoff=0.8.binning.bench.json
│                   ├── --rel-cutoff=0.8.binning.bench.tsv
│                   ├── --rel-cutoff=0.8.binning.bioboxes.gz
│                   ├── --rel-cutoff=0.8.binning.log
│                   └── --rel-cutoff=0.8.rep
└── kmcp
    └── 0.9.4
        └── mende.10species.10K
            └── bac_rs_refgen
                └── default
                    ├── default
                    │   ├── default.profiling.bench.json
                    │   ├── default.profiling.bench.tsv
                    │   ├── default.profiling.bioboxes.gz
                    │   └── default.profiling.log
                    ├── default.binning.bench.json
                    ├── default.binning.bench.tsv
                    ├── default.binning.bioboxes.gz
                    └── default.binning.log

*.profiling.bioboxes.gz contains the standardized profiling output in bioboxes format.
*.binning.bioboxes.gz contains the standardized binning output in bioboxes format.
*.bench.json contains the runtime metrics in JSON format. If repeat > 1 in the config file, only the fastest run is selected. This file will be updated in the next step (evaluation).
*.bench.tsv contains the raw benchmark metrics from Snakemake. If repeat > 1 in the config file, one line for each run will be reported.
*.log contains the STDOUT and STDERR from the run.

Check the config/classify_example.yaml for more examples on how to use the configuration file. Multiple databases, samples, range of parameters and others can be configured to be executed in the same run.

Evaluations

Evaluation will calculate metrics for binning and profiling procedures. It requires ground truth files for each sample

Create config/evals_test.yaml:

workdir: "example/classify/"
threads: 8

samples:
  "mende.10species.10K":
    "binning": "../../files/illumina_10species.10K.binning.bioboxes.gz"
    "profiling": "../../files/illumina_10species.profile.bioboxes.gz"

# Optional, contents of the database for some metrics
dbs:
  "bac_rs_refgen": "../build/ganon/2.0.0/bac_rs_refgen/default/ganon_db.tax"

# Ranks to evaluate
ranks:
  - superkingdom
  - phylum
  - class
  - order
  - family
  - genus
  - species

taxonomy: "ncbi"
taxonomy_files: "../bac_rs/refgen/taxdump.tar.gz"

# Set one or more thresholds for evaluation metrics [0-100]
threhsold_profiling:
  - 0

threhsold_binning:
  - 0
  - 0.05
  - 1

Verify run with --dry-run:

snakemake -s metabench/evals.smk --configfile config/evals_test.yaml --cores 8 --use-conda --dry-run

Run it:

snakemake -s metabench/evals.smk --configfile config/evals_test.yaml --cores 8 --use-conda

If everything finished correctly, the following files will be created:

Files

$ tree -A example/classify/

example/classify/
├── ganon
│   └── 2.0.0
│       └── mende.10species.10K
│           └── bac_rs_refgen
│               ├── default
│               │   ├── --rel-cutoff=0.25
│               │   │   ├── default.profiling.bench.json
│               │   │   ├── default.profiling.bench.tsv
│               │   │   ├── default.profiling.bioboxes.gz
│               │   │   ├── default.profiling.evals.log
│               │   │   ├── default.profiling.log
│               │   │   └── default.profiling.updated_json
│               │   ├── --rel-cutoff=0.25.binning.bench.json
│               │   ├── --rel-cutoff=0.25.binning.bench.tsv
│               │   ├── --rel-cutoff=0.25.binning.bioboxes.gz
│               │   ├── --rel-cutoff=0.25.binning.evals.log
│               │   ├── --rel-cutoff=0.25.binning.log
│               │   ├── --rel-cutoff=0.25.binning.updated_json
│               │   ├── --rel-cutoff=0.25.rep
│               │   ├── --rel-cutoff=0.8
│               │   │   ├── default.profiling.bench.json
│               │   │   ├── default.profiling.bench.tsv
│               │   │   ├── default.profiling.bioboxes.gz
│               │   │   ├── default.profiling.evals.log
│               │   │   ├── default.profiling.log
│               │   │   └── default.profiling.updated_json
│               │   ├── --rel-cutoff=0.8.binning.bench.json
│               │   ├── --rel-cutoff=0.8.binning.bench.tsv
│               │   ├── --rel-cutoff=0.8.binning.bioboxes.gz
│               │   ├── --rel-cutoff=0.8.binning.evals.log
│               │   ├── --rel-cutoff=0.8.binning.log
│               │   ├── --rel-cutoff=0.8.binning.updated_json
│               │   └── --rel-cutoff=0.8.rep
│               └── --max-fp=0.0001
│                   ├── --rel-cutoff=0.25
│                   │   ├── default.profiling.bench.json
│                   │   ├── default.profiling.bench.tsv
│                   │   ├── default.profiling.bioboxes.gz
│                   │   ├── default.profiling.evals.log
│                   │   ├── default.profiling.log
│                   │   └── default.profiling.updated_json
│                   ├── --rel-cutoff=0.25.binning.bench.json
│                   ├── --rel-cutoff=0.25.binning.bench.tsv
│                   ├── --rel-cutoff=0.25.binning.bioboxes.gz
│                   ├── --rel-cutoff=0.25.binning.evals.log
│                   ├── --rel-cutoff=0.25.binning.log
│                   ├── --rel-cutoff=0.25.binning.updated_json
│                   ├── --rel-cutoff=0.25.rep
│                   ├── --rel-cutoff=0.8
│                   │   ├── default.profiling.bench.json
│                   │   ├── default.profiling.bench.tsv
│                   │   ├── default.profiling.bioboxes.gz
│                   │   ├── default.profiling.evals.log
│                   │   ├── default.profiling.log
│                   │   └── default.profiling.updated_json
│                   ├── --rel-cutoff=0.8.binning.bench.json
│                   ├── --rel-cutoff=0.8.binning.bench.tsv
│                   ├── --rel-cutoff=0.8.binning.bioboxes.gz
│                   ├── --rel-cutoff=0.8.binning.evals.log
│                   ├── --rel-cutoff=0.8.binning.log
│                   ├── --rel-cutoff=0.8.binning.updated_json
│                   └── --rel-cutoff=0.8.rep
└── kmcp
    └── 0.9.4
        └── mende.10species.10K
            └── bac_rs_refgen
                └── default
                    ├── default
                    │   ├── default.profiling.bench.json
                    │   ├── default.profiling.bench.tsv
                    │   ├── default.profiling.bioboxes.gz
                    │   ├── default.profiling.evals.log
                    │   ├── default.profiling.log
                    │   └── default.profiling.updated_json
                    ├── default.binning.bench.json
                    ├── default.binning.bench.tsv
                    ├── default.binning.bioboxes.gz
                    ├── default.binning.evals.log
                    ├── default.binning.log
                    └── default.binning.updated_json

*.bench.json were updated with evaluation metrics.
*.evals.log contains the STDOUT and STDERR from the evaluation run.
*.updated_json flag file to set the evaluation is over and updated the correspondent .json file

Check the config/evals_example.yaml for more examples on how to use the configuration file. Multiple samples and thresholds can be configured to be executed in the same run.

Plotting

Finally, to visualize the benchmark, plot the results:

scripts/plot.py -i example/ --output example/dashboard.html

Open the example/dashboard.html in your browser and explore the results.

Name		Name	Last commit message	Last commit date
Latest commit History 105 Commits
config		config
envs		envs
files		files
metabench		metabench
scripts		scripts
tools		tools
.gitignore		.gitignore
LICENSE		LICENSE
README.md		README.md

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MetaBench

Installation and requirements

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Classify (binning profiling)

Evaluations

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MetaBench

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Usage example

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Classify (binning profiling)

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Plotting

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