MetaCAT

Metagenome Clustering and Association Tool.

Dependencies

• CheckM2

• CuPy

• FragGeneScan

• GTDB-Tk

• Hmmer

• Mash

• FastANI

• skani

Dependencies used for clutering sequneces

FragGeneScan, hmmpress and hmmsearch (from the Hmmer tool) are used in the seed command of MetaCAT.

MetaCAT uses built-in versions of FragGeneScan, hmmpress, and hmmsearch by default,
if you are running on a supported platform (i.e., x86_64 Linux or arm macOS).

Otherwise, you need to compile them manually and ensure they are callable by MetaCAT.

You can specify their paths using --fraggenescan, --hmmpress and --hmmsearch options.

Note that the built-in binaries are only accessible to the seed command and cannot be called by external programs.

Dependencies used for estimating cluster quality

CheckM2 is used in the checkm2 command of MetaCAT.

By default, MetaCAT uses the checkm2 from the environment.

You can specify its path using the --checkm2 option.

CheckM2 and its database must be installed manually.

Detailed installation instructions can be found here.

For more details, please visit the CheckM2 repository.

Dependencies used for classifying clusters

GTDB-Tk is used in the gtdbtk command of MetaCAT.

By default, MetaCAT uses gtdbtk from the environment.

You can specify its path using the --gtdbtk option.

GTDB-Tk and its database must be installed manually.

Detailed installation instructions can be found here.

For more details, please visit the GTDB-Tk repository.

Dependencies used for selecting representatives

Mash or FastANI or Skani is used in the representative command of MetaCAT.

By default, MetaCAT uses the built-in Mash binary
if you are running on a supported platform (i.e., x86_64 Linux or arm macOS).

Otherwise, you need to compile Mash manually and ensure it is callable by MetaCAT.

You can specify its path using the --mash option.

Note that the built-in binaries are only accessible to the representative command and cannot be called by external programs.

Additionally, we provide FastANI and Skani as alternatives (--engine fastANI|skani) in representative command.

To use FastANI or Skani, you need to compile it manually.

MetaCAT uses FastANI or Skani from the environment by default.

You can specify its path using the --fastani or --skani option.

Install MetaCAT

pip3 install https://github.com/liu-congcong/MetaCAT/releases/download/v1.0.3/metacat-1.0.3-py3-none-any.whl

GPU version for MetaCAT

To enable the GPU for MetaCAT, you need to install CuPy.

pip3 install cupy-cudaXXX

Documentation

HERE.

Examples

HERE.

Datasets for Review

HERE.

Updates

v1.0.0

The first release.

v1.0.1

Add --bam-suffix in coverage command.

Add --fasta-suffix in cluster2mapping command.

Add --input-suffix in indexBam command.

Add --fasta-suffix in representative command.

Add --bam-suffix and --mapping-suffix in abundance command.

Add --input-suffix in variant command.

Add --input-suffix in checkm2 command.

Add --input-suffix in gtdbtk command.

v1.0.2

Fixed a bug in the checkm2 command that occurred when handling a large number of input files.

v1.0.3

Fixed a bug that could potentially cause a segmentation fault.

Support skani.

Rewrite indexBam.