Compile

git clone https://github.com/RabbitBio/RabbitUniq
cd RabbitUniq
make

Parameters

usage: RabbitUniq.py [-h] [--workspace WORKSPACE] --infile_list INFILE_LIST --outfile OUTFILE [--gu_worker GU_WORKER] [--kmer_len KMER_LEN] [--bin_num BIN_NUM]
                     [--exclude_last] [--output_char]

RabbitUniq

optional arguments:
  -h, --help            show this help message and exit
  --workspace WORKSPACE, -w WORKSPACE
                        workspace directory the bin files stored [default: workspace]
  --infile_list INFILE_LIST, -l INFILE_LIST
                        input file list, one line per file
  --outfile OUTFILE, -o OUTFILE
                        out put file
  --gu_worker GU_WORKER, -n GU_WORKER
                        The number of worker thread when generate unique kmer [default: 20]
  --kmer_len KMER_LEN, -k KMER_LEN
                        Unique k-mer length [default: 25]
  --bin_num BIN_NUM, -b BIN_NUM
                        Number of bin files to be store, from 64 to 2000[default: 512]
  --exclude_last, -e    Exclude the last element in infile_list when output
  --uniq_ref_num UNIQ_REF_NUM, -u UNIQ_REF_NUM
                        Threshold considered as unique kmer, default is 1
  --output_char, -c     Output the unique k-mer collection in character-based file instead of binary file (slower, so not recommended)

Run RabbitUniq

Generate unique kmer

cat $REF_FILE_PATH >> ${infile_list}
time${RabbitUniq_PATH }/RabbitUniq.py \
  --infile_list  ${infile_list} \
  --outfile  ${outname}.bin \
  -n 20 -k 25 -b 2000 \

exclude the reference file

Add the reference file to the end of input list file list, and run RabbitUniq with parameter --exclude_last.

cat $REF_FILE_PATH >> ${infile_list}
time${RabbitUniq_PATH }/RabbitUniq.py \
  --infile_list  ${infile_list} -19. list \
  --outfile  ${outname}.bin \
  -n 20 -k 25 -b 512 \
  --exclude_last\