Running and Verifying SOAPdenovo

Procedure

1. Use PuTTY to log in to the server as the root user.
2. Copy the test case files and go to the test directory.

   cp B17NC_R1.fq.gz /path/to/SOAPDENOVO/SOAPdenovo2-r241
   cp B17NC_R2.fq.gz /path/to/SOAPDENOVO/SOAPdenovo2-r241
   cd /path/to/SOAPDENOVO/SOAPdenovo2-r241

3. Decompress the case files.

   gzip -d B17NC_R1.fastq.gz
   gzip -d B17NC_R2.fastq.gz

4. Clear the cache.

   echo 3 > /proc/sys/vm/drop_caches

5. Create a configuration file.
   1. Create a configuration file.

      vi config_file

   2. Press i to enter the insert mode and add the following content:

      max_rd_len=100
      [LIB]
      avg_ins=200
      reverse_seq=0
      asm_flags=3
      rd_len_cutoff=100
      rank=1
      q1=B17NC_R1.fastq
      q2=B17NC_R2.fastq

   3. Press Esc, type :wq!, and press Enter to save the file and exit.
6. Execute the test case.

   { time -p ./SOAPdenovo-63mer all -s config_file -K 63 -p 96 -R -o graph_prefix; } 2>&1 |tee  SOAPdenovo.log

   Check the value of real (in seconds) in the SOAPdenovo.log file. A smaller value indicates higher performance.

   Figure 1 is an example of the output result.

   Figure 1 An example result