HiFine: integrating Hi-c-based and shotgun-based methods to reFine binning of metagenomic contigs

Introduction

HiFine is a pipeline to refine the binning results of metagenomic contigs by integrating both Hi-C-based and shotgun-based binning tools. HiFine designs a strategy of fragmentation for the original bin sets derived from the Hi-C-based and shotgun-based binning methods, which considerably increases the purity of initial bins, followed by merging fragmented bins and recruiting unbinned contigs.

Install and Setup

conda

We recommend using conda to run HiFine.

After installing Anaconda (or miniconda), Users can clone the repository with git:

git clone https://github.com/dyxstat/HiFine.git

Once complete, you can enter the repository folder and then create a HiFine environment using conda:

# enter the HiFine folder
cd HiFine
# Construct environment
conda env create -f HiFine_linux_env.yaml 
or
conda env create -f HiFine_osx_env.yaml
# Enter the environment
conda activate HiFine_env

Preparation

Deriving the initial sets from different types of binning methods

Two initial binning sets are needed, corresponding to two folders. One folder contains bins generated by a Hi-C-based binning method and the second folder includes bins constructed by a shotgun-based binning pipeline.

Generating metagenomic Hi-C contact maps normalized by HiCzin

• If you employs HiCBin to bin the contigs, you can directly get access to normalized Hi-C contact maps through the file ‘HiCzin_normalized_contact.gz’ in the output directory of HiCBin.
• If you use other Hi-C-based binning methods such as ProxiMeta or bin3C, you need to run the HiCzin software (https://github.com/dyxstat/HiCzin) to generate normalized Hi-C contact maps. The normalized Hi-C contacts and other needed contig information are stored in the file 'HiCzin_normalized_contact.gz' from the output directory of HiCzin software.

Then you can move the file 'HiCzin_normalized_contact.gz' to the directory of HiFine folder.

Usage

Implement the HiFine pipeline

python ./hifine.py refine [Parameters] HiC_folder Shotgun_folder HiC_contacts Contig_file Output_directory

Parameters

--min-binsize: Minimum bin size of shared bins [default: 500000]
--min-complete: Minimum bin size of relatively complete bins [default: 500000]
--min-frac: Fraction to determine the relatively complete bins [default: 0.8]
--alpha: hyperparameter in step2 [default: 0.6]
--beta: hyperparameter in step3 [default: 0.3]
--bin3C: Whether the Hi-C-based binning method is bin3C [default: False]
--cover: Cover existing files
-v: Verbose output

Input File

• HiC_folder: a folder path containing bins generated by a Hi-C-based binning method
• Shotgun_folder: a folder path including bins constructed by a shotgun-based binning method
• HiC_contacts: Hi-C contact maps normalized by HiCzin (i.e., file 'HiCzin_normalized_contact.gz')
• Contig_file: a fasta file of the assembled contig (e.g. final.contigs.fa)

Example

python ./hifine.py refine -v hicbin_bin_folder metabat2_bin_folder HiCzin_normalized_contact.gz final.contigs.fa out

Specically, if you employs bin3C as the Hi-C-based binning method, use

python ./hifine.py refine --bin3C -v bin3C_bin_folder metabat2_bin_folder HiCzin_normalized_contact.gz final.contigs.fa out

The results of the pipeline action are all in the 'out' directory.

Output File

• HIFINE_BIN: Final refined genomic bins by HiFine
• hifine_cluster.txt: Specific group labels of binned contigs
• hifine.log: log file of the specific implementation information of HiCBin

Contacts and bug reports

If you have any questions or suggestions, welcome to contact Yuxuan Du (yuxuandu@usc.edu).

Copyright and License Information

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.