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Fast Assembler Workflow for MitoGenome

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

Use in Docker

# help
docker run --rm -it suqingdong/fast-mito-assembler:latest
docker run --rm -it suqingdong/fast-mito-assembler:latest FastMitoAssembler run

# use FastMitoAssembler
docker run --rm -it \
  -v $PWD/data:/work/data \
  -v $PWD/config.yaml:/work/config.yaml \
  suqingdong/fast-mito-assembler \
  FastMitoAssembler run --configfile config.yaml --dryrun

# use Snakemake
docker run --rm -it \
  -v $PWD/data:/work/data \
  -v $PWD/config.yaml:/work/config.yaml \
  suqingdong/fast-mito-assembler \
  snakemake -s /opt/miniconda3/envs/FastMitoAssembler/lib/python3.9/site-packages/FastMitoAssembler/smk/main.smk --configfile config.yaml --dryrun

config.yaml

reads_dir: 'data'
samples: ['2222-4']
fq_path_pattern: '{sample}/{sample}_1.clean.fq.gz'
seed_input: '2222-4_deep_detected_mito.fas'

Use in DockerCompose

# docker-compose.yml
version: "3"

services:
  fast_mito_assembler:
    image: suqingdong/fast-mito-assembler:latest
    volumes:
      - ./data:/work/data
      - ./config.yaml:/work/config.yaml
      - ./2222-4_deep_detected_mito.fas:/work/2222-4_deep_detected_mito.fas
    command: FastMitoAssembler run --configfile config.yaml --dryrun
docker-compose up