Dnaapler实战：如何统一环状微生物基因组的起始位置

# 创建一个名为Dnaapler的conda环境，并安装dnaapler
conda create -n Dnaapler -c conda-forge -c bioconda dnaapler 
# conda install 直接安装
conda install -c bioconda dnaapler
# pip install 安装
pip install dnaapler
# 激活环境
conda activate Dnaapler  

dnaapler -h
Usage: dnaapler [OPTIONS] COMMAND [ARGS]...

Options:
  -h, --help     Show this message and exit.
  -V, --version  Show the version and exit.

Commands:
  all         Reorients contigs to begin with any of dnaA, repA, terL or
              archaeal COG1474 Orc1/cdc6
  archaea     Reorients your genome to begin with the archaeal COG1474
              Orc1/cdc6 origin recognition complex gene
  bulk        Reorients multiple genomes to begin with the same gene
  chromosome  Reorients your genome to begin with the dnaA chromosomal
              replication initiation gene
  citation    Print the citation(s) for this tool
  custom      Reorients your genome with a custom database
  largest     Reorients your genome the begin with the largest CDS as called
              by pyrodigal
  mystery     Reorients your genome with a random CDS
  nearest     Reorients your genome the begin with the first CDS as called by
              pyrodigal
  phage       Reorients your genome to begin with the terL large terminase
              subunit
  plasmid     Reorients your genome to begin with the repA replication
              initiation gene

自动识别并重定向多种类型的 contig，可识别 dnaA、repA、terL 或古菌 COG1474 Orc1/cdc6

dnaapler all -h
Usage: dnaapler all [OPTIONS]

Options:
  -h, --help               Show this message and exit.
  -V, --version            Show the version and exit.
  -i, --input PATH         Path to input file in FASTA or GFA format
                           [required]
  -o, --output PATH        Output directory   [default: output.dnaapler]
  -t, --threads INTEGER    Number of threads to use with MMseqs2  [default: 1]
  -p, --prefix TEXT        Prefix for output files  [default: dnaapler]
  -f, --force              Force overwrites the output directory
  -e, --evalue TEXT        E-value for MMseqs2  [default: 1e-10]
  --ignore TEXT            Text file listing contigs (one per row) that are to
                           be ignored OR comma separated list of contig names
                           to ignore OR '-' to read from stdin
  --db, --database TEXT    Lets you choose a subset of databases rather than
                           all 4. Must be one of: 'all', 'dnaa', 'repa',
                           terl', 'cog1474', 'dnaa,repa', 'dnaa,terl',
                           'repa,terl',  'dnaA,cog1474', 'cog1474,terl',
                           'cog1474,repa', 'dnaa,cog1474,repa',
                           'dnaa,cog1474,terl' or 'cog1474,repa,terl'
                           [default: all]
  -c, --custom_db PATH     FASTA file with amino acids that will be used as a
                           custom MMseqs2 database to reorient your sequence
                           however you want.
  -a, --autocomplete TEXT  Choose an option to autocomplete reorientation if
                           MMseqs2 based approach fails. Must be one of: none,
                           mystery, largest, or nearest [default: none]
  --seed_value INTEGER     Random seed to ensure reproducibility.  [default:
                           13]

查看 dnaapler all 的帮助信息

# 统一细菌环状染色体的起始位置，以 dnaA 基因为起点进行重定向
dnaapler chromosome -i chromosome.fasta -o C333 -t 8 -p C333 -f 
# 自动识别输入序列中的细菌染色体、质粒、噬菌体或古菌环状 contig，并统一其起始位置
dnaapler all -i scoffold.fasta -o C333 -t 8 -p C333 -f
# 将噬菌体环状基因组重定向至 terL 大末端酶亚基基因位置
dnaapler phage -i sa3int_phage.fasta -o sa3int -t 8 -p sa3int -f

最重要的结果文件，这是重定向后的 FASTA 序列