Chaser

Chaser is a Conda-based snakemake script available for rapid and low-pollution plant mitochondrial genome assembly.

Assembly flow diagram

Download and deploy the conda environment synchronized with the development environment

The software will be installed include minimap2 samtools miniasm GetOrganell flye bwa-mem2 seqkit blast+ pilon racon

Use the following command use conda to resolve their dependency. Make sure that conda is deployed on your terminal before using it.

wget https://cdn.jsdelivr.net/gh/DaiWeiKIB/chaser@main/chaser_env.yml    
conda env create -f chaser_env.yml  
conda activate chaser  

The default script configuration file can be obtained using the following command

wget https://cdn.jsdelivr.net/gh/DaiWeiKIB/chaser@main/config.yaml  

Fill in the genome information according to the comments in config.yaml

Long_reads_dir:
    /home/daiwei/Oryza_sativa/CRR306311.fasta    #Directory path of single molecule sequencing data file path only with fasta format
Short_reads_dir1:
    /home/daiwei/Oryza_sativa/CRR306398_f1.fq.gz    #Directory path of Illumina sequencing data
Short_reads_dir2:
    /home/daiwei/Oryza_sativa/CRR306398_r2.fq.gz
Number_of_threads: 
    10
Maximum_memory:
    10G
Seed_dir:
    /home/daiwei/Oryza_sativa/NC_011033.1.fasta    #Mitochondrial genome data of related species could be selected as seed
Long_reads_platform:
    ont    #Available options: ont(Oxford Nanopore Sequencing technology) / pb(Pacbio biosciences)
Long_reads_type:
    --nano-raw    #Available options: --pacbio-raw (PacBio regular CLR reads <20% error) / --pacbio-corr(PacBio reads <3% error) / --pacbio-hifi (PacBio HiFi reads <1% error) / --nanoraw (ONT regular reads <20% error) / --nano-corr (ONT reads <3% error)/ --nano-hq (ONT high-quality reads <5% error)
Estimated_genome_size:
    0.5m    #Estimated genome size given by the user in this field(According to the reference genome)

Download the relevant process file to customize the script based on the comments

wget https://cdn.jsdelivr.net/gh/DaiWeiKIB/chaser@main/chaser

Start assembly

snakemake -s chaser -c {number of threads}

Test data set

This pipeline was validated using publicly accessible illumina, nanopore, and Pacbio Hifi sequencing data. Arabidopsis thaliana and Oryza sativa were registered in the public databases of the China National Center for Bioinformation (CNCB) and the US National Center for Biotechnology Information (NCBI).

Test assembly result

Due to the structural variability of the mitochondrial genome, the assembly presents realistic and reasonable results.

Contact

Please communicate me with email address: daiwei20@mails.ucas.ac.cn