crac -i <index\_file> -k <int> -r <reads\_file1> -o <output\_file> --nb-threads <int>


  • -i  is the name of the index previously built with the crac-index binary file. Note that crac-index construct the structure  with its configuration so only the prefix  must be specified (without extension) to consider the structure and the configuration files both in CRAC.
  • -r [reads\_file2] is the source(s) of the FASTA or FASTQ file(s) containing the reads. Note that the number of files depends if single or paired-reads. The input file may also be compressed using gzip.
  • -k  is the length of the k-mer to be used to map the reads on the reference . Note that the condition (k < m) is necessary and reads (or both paired reads) are ignored if m < k. It must be chosen to ensure (as much as possible) that a k-mer has a very high probability to occur a single time on the genome.
  • -o  (or --sam ) is the output file in SAM format or print on STDOUT with “-o -“ argument. See the Documentation of SAM format in CRAC for more details.
  • --nb-threads  is the number of threads to run crac, computational time is almost divided by the number of threads.

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