FastMitoAssembler 1.0.1

Fast Assembler Workflow for MitoGenome

Fast Assembler Workflow for MitoGenome

FastMitoAssembler is a software for fast, accurate assembly of mitochondrial genomes and generation of annotation documents.

Softwares

• MEANGS
• NOVOplasty
• GetOrganelle
• SPAdes
• MitoZ
• NCBI-Blast

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 genbank

2. activate environment

source $(dirname `which conda`)/activate FastMitoAssembler

3. install FastMitoAssembler

python -m pip install -U FastMitoAssembler
# or
python -m pip install -U dist/FastMitoAssembler*whl

Prepare

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 databaes
FastMitoAssembler prepare organelle -a all  # config all databases

### Usage
#### Use with Client
```bash
FastMitoAssembler

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 --dryrun

Use 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 --dryrun

Use in Docker

docker