AutoSGRS is a tool that automatically searches for repeated sequences of any frequency in any genome

We suggest using Python 3.8 for AutoSGRS.

pip install -r requirements.txt

wget https://bowtie-x64-linux.tar.gz -O ~/bowtie-x64-linux.tar.gz

tar -zxvf bowtie-x64-linux.tar.gz

export PATH=~/bowtie/bin:$PATH

Input:

• Step 1: Upload destination genome file(fasta)
• Step 2: provide the necessary configuration information.
  • Example configuration:

    {
      "kmer_size":100,
      "Repetitive_quantity":15,
      "genome_name":"Yarrowia_lipolytica"
    }

Execute:

python find_repeats_with_kmers.py

Output:

• xxx.csv These files will be generated in the XXX/AutoSGRS/output directory.