Fast Assembler Workflow for MitoGenome
FastMitoAssembleris a software for fast, accurate assembly of mitochondrial genomes and generation of annotation documents.
Installation
1. create environment
# method 1: use conda [slowly and need large resources]
conda env create -f environment.yml
# method 2: use mamba [*recommended*]
conda install mamba -c conda-forge -y
mamba env create -f environment.yml
# method 3: install manually
conda config --add channels yccscucib
conda config --add channels bioconda
conda config --add channels conda-forge
mamba create -n FastMitoAssembler -y python==3.9.*
mamba install -n FastMitoAssembler -y snakemake
mamba install -n FastMitoAssembler -y NOVOPlasty
mamba install -n FastMitoAssembler -y GetOrganelle
mamba install -n FastMitoAssembler -y spades
mamba install -n FastMitoAssembler -y blast
mamba install -n FastMitoAssembler -y mitoz
mamba install -n FastMitoAssembler -y seqkit
mamba install -n FastMitoAssembler -y meangs
mamba install -n FastMitoAssembler -y click
mamba install -n FastMitoAssembler -y jinja2
mamba install -n FastMitoAssembler -y pyyaml
source $(dirname `which conda`)/activate FastMitoAssembler
python -m pip insatll genbank2. activate environment
source $(dirname `which conda`)/activate FastMitoAssembler3. install FastMitoAssembler
python -m pip install -U FastMitoAssembler
# or
python -m pip install -U dist/FastMitoAssembler*whlPrepare Database
FastMitoAssembler prepare
# 1. prepare ete3.NCBITaxa
FastMitoAssembler prepare ncbitaxa # download taxdump.tar.gz automaticlly
FastMitoAssembler prepare ncbitaxa --taxdump_file taxdump.tar.gz
# 2. prepare database for GetOrganelle
FastMitoAssembler prepare organelle --list # list configured databases
FastMitoAssembler prepare organelle -a animal_mt # config a single database
FastMitoAssembler prepare organelle -a animal_mt -a embplant_mt # config multiple databases
FastMitoAssembler prepare organelle -a all # config all databasesRun Workflow
config.yaml example:
reads_dir: '../data/'
samples: ['2222-4']
fq_path_pattern: '{sample}/{sample}_1.clean.fq.gz' # the reads 1 path pattern relative to `reads_dir`see the main Snakefile and Template configfile with: FastMitoAssembler --help
Use with Client
FastMitoAssembler --help
FastMitoAssembler run --help
# run with configfile [recommended]
FastMitoAssembler run --configfile config.yaml
# run with parameters
FastMitoAssembler run --reads_dir ../data --samples S1 --samples S2
# set cores
FastMitoAssembler run --configfile config.yaml --cores 8
# dryrun the workflow
FastMitoAssembler run --configfile config.yaml --dryrunUse with Snakemake
# the `main.smk` and `config.yaml` template can be found with command: `FastMitoAssembler`
snakemake -s /path/to/FastMitoAssembler/smk/main.smk -c config.yaml --cores 4
snakemake -s /path/to/FastMitoAssembler/smk/main.smk -c config.yaml --cores 4 --printshellcmds
snakemake -s /path/to/FastMitoAssembler/smk/main.smk -c config.yaml --printshellcmds --dryrunUse with Docker
Example Results Directory
-
[*]represents the main result
result/
└── 2222-4
├── 1.MEANGS
│  ├── 2222-4
│  ├── 2222-4_deep_detected_mito.fas [*]
│  └── scaffold_seeds.fas
├── 2.NOVOPlasty
│  ├── config.txt
│  ├── Contigs_1_2222-4.fasta
│  ├── 2222-4.novoplasty.fasta [*]
│  ├── contigs_tmp_2222-4.txt
│  └── log_2222-4.txt
├── 3.GetOrganelle
│  ├── 2222-4_1.5G.fq.gz
│  ├── 2222-4_2.5G.fq.gz
│  ├── 2222-4.fq1.stats.txt
│  ├── animal_mt.get_organelle.fasta [*]
│  └── organelle
└── 4.MitozAnnotate
├── 2222-4.animal_mt.get_organelle.fasta.result [*]
└── tmp_2222-4_animal_mt.get_organelle.fasta_mitoscaf.fa
