MetaCompass v2.0-beta

Publications

Luan T, Cepeda V, Liu B, Bowen Z, Ayyangar U, Almeida M, Hill CM, Koren S, Treangen TJ, Porter A, Pop M. MetaCompass: Reference-guided Assembly of Metagenomes. ArXiv [Preprint]. 2024 Mar 3:arXiv:2403.01578v1. PMID: 38903742; PMCID: PMC11188144.

Victoria Cepeda, Bo Liu, Mathieu Almeida, Christopher M. Hill, Sergey Koren, Todd J. Treangen, Mihai Pop. bioRxiv 212506; doi: https://doi.org/10.1101/212506

Installation

1. Check if you have all the requirements.

2. Clone the repository

   git clone 'https://github.com/marbl/MetaCompass.git'
   

3. Install conda and create a conda environment using the metacompass_environment.yml file

   conda env create -f metacompass_environment.yml
   

4. Set up reference database.

   You have the option to either generate a reference database on your own or utilize the one provided by us. Please refer to the instructions here for guidance on how to proceed.

Detailed installation instructions are here.

Usage

This provides a quick overview of running the Metacompass.

0. Ensure that the overall parameters mentioned in nextflow.config are correctly set for your environment. In the very least, you should make sure that the parameters for the executor are set correctly. As distributed, the assumption is the code will be run with the local executor and a queue size of 2 (number of "parallel" processes spawned by Nextflow).

Note that this file also contains the key parameters used by MetaCompass for different parts of the pipeline. Detailed documentation of these parameters is forthcoming.

2. Set up your input data and reference database paths.

3. Create an output directory. Note: if output directory is not specified, it defaults to "results"

4. Run Metacompass Nextflow script using appropriate parameters.

    
    nextflow run metacompass2.nf \
    --reference_db "${ref_db_path}" \ # [required]
    --forward "$forward_read" \ # [required]
    --reverse "$reverse_read" \ # [required]
    -output-dir "$output_folder" \ # [required]
    --threads 8 \ # [optional] by default it is 16
    --trace_file_name "$output_folder/trace.txt" \ # [optional] 
    -with-timeline "$output_folder/timeline.html" \ # [optional]

Parameter description: <br/>

• forward : Path to the file with forward reads, providing sequence information from one end of the DNA fragment in a specific direction.
• reverse : Path to the file with reverse reads, representing sequence information from the opposite end of the DNA fragment in the reverse direction.
• output_dir : The output directory or file path where the results will be stored.
• threads: The number of threads to use during reference-guided assembly with Pilon. <br/> <br/> Full parameter configuration can be found here

Detailed usage instructions are here