consensusLJA

Overview

consensusLJA is an assembler designed to generate high-quality consensus genome assemblies using PacBio high-fidelity (HiFi) reads alone. This tool aims to simplify the assembly process for non-human genomes by producing nearly complete haplotype-mixed consensus assemblies, which are cost-effective and require fewer sequencing technologies compared to diploid assemblies.

Features

• Generates consensus genome assemblies using only HiFi reads
• Provides nearly complete assemblies with a mosaic of two haplotypes
• Reduces the complexity and cost associated with diploid assembly generation
• Tailored for non-human genomes, though applicable to any genome sequencing projects

Installation

To install consensusLJA (cLJA), follow the steps below to install the required dependencies, clone the repository, and build the tool.

Steps:

1. Install Dependencies:
   Install the required dependencies to ensure proper functionality:

   • gcc: tested on v11.4.0
   • minimap2: v2.21 (For creating BAM files)
   • samtools: v1.11 (For processing BAM files)
   • pysam: v0.22.1 (For processing BAM files)

   These dependencies can be installed using Conda, which will create a new environment named cLJA (if you already installed these dependencies, skip this step):

   conda env create -f requirements.yml

2. Install LJA assembler:
   cLJA uses the assembly graph generated by LJA. So LJA assembler (the experimental branch) is required.

   git clone https://github.com/AntonBankevich/LJA.git -b experimental
   cd LJA
   cmake . && make

3. Activate the Environment:
   Activate the clja Conda environment:

   conda activate clja

4. Clone the Repository:
   Clone the consensusLJA repository:

   git clone https://github.com/ZhangZhenmiao/consensusLJA.git

5. Build the Tool:
   Navigate to the repository and build the tool using make:

   cd consensusLJA && make
   chmod +x cLJA get_reference.py

6. Add cLJA to Your PATH (Optional):
   Add the cLJA executable to your environment's PATH:

   export PATH="`pwd`":$PATH

   Note: You can add this line to your ~/.bashrc for convenience, so that cLJA is available in your PATH every time you start a new shell session (optional):

   echo -e '\nexport PATH="'$(pwd)'":$PATH' >> ~/.bashrc

Usage

With HiFi reads, first assemble using LJA. See more details in the LJA manual:

lja [options] -o <output_dir> --reads <reads_file> [--reads <reads_file2> ...]

The output directory will contain the following structure:

<output_dir>/
│
├── 00_CoverageBasedCorrection/
├── 01_TopologyBasedCorrection/
│   ├── final_dbg.dot
│   ├── final_dbg.fasta
├── 02_MDBG/
│   ├── mdbg_edge_seqs.fasta
├── 03_Polishing/
├── assembly.fasta
├── lja.log
├── mdbg.gfa
└── version.txt

After assembling with LJA, you can use cLJA to process the relevant files (LJA will be integrated to cLJA in later versions).

cLJA Command Syntax:

cLJA --dot=<string> --fasta=<string> --multidbg=<string> --output=<string>

Parameters:

• -d, --dot <string>:
  This specifies the graph.dot file, typically found under 01_TopologyBasedCorrection/final_dbg.dot. It represents the condensed de Bruijn graph of LJA.
  Example: --dot=final_dbg.dot, -d final_dbg.dot

• -f, --fasta <string>:
  This expects the graph.fasta file, found under 01_TopologyBasedCorrection/final_dbg.fasta. It contains the sequences of the edges in the graph of LJA.
  Example: --fasta=final_dbg.fasta, -f final_dbg.fasta

• -m, --multidbg <string>:
  Specifies the multidbg file, which contains the edge sequences in the multiplex de Bruijn graph of LJA, found under 02_MDBG/mdbg_edge_seqs.fasta.
  Example: --multidbg=mdbg_edge_seqs.fasta, -m mdbg_edge_seqs.fasta

• -o, --output <string>:
  The output directory where the results will be stored. This directory must be new and should not contain any prior data to avoid conflicts or overwrites.
  Example: --output=/path/to/output_directory, -o /path/to/output_directory

• -?, --help:
  Prints a help message that includes information about all the available options. Use this if you want a quick summary of how to use the tool.
  Example: --help

Example Usage:

In the example folder under this google drive link, there is a small test dataset. The output directory from LJA has already been generated in LJA_output. You can run cLJA using the command line below:

cLJA -d LJA_output/01_TopologyBasedCorrection/final_dbg.dot -f LJA_output/01_TopologyBasedCorrection/final_dbg.fasta -m LJA_output/02_MDBG/mdbg_edge_seqs.fasta -o cLJA_output

In this example, cLJA will process the final_dbg.dot, final_dbg.fasta, and mdbg_edge_seqs.fasta files, and output the results into the cLJA_output directory. It will generate the final consensus assembly in the file cLJA_output/graph.final.fasta (currently it's homopolymer collapsed contigs; we will uncompress them in later versions).

If you encounter any issues or errors, please feel free to open an issue on the repository.