SOAP

• 軟體來源：​http://soap.genomics.org.cn/soap1/

【說明】

【安裝】

   wget http://soap.genomics.org.cn/soap1/soap_1.11.tar.gz
   tar zxvf sim4.tar.gz

【路徑】

   /opt/soap1

【測試】

   soap -a soap_test_reads.txt -d reference.fasta -o output.txt -s 10 -r 0

【結果】

• 輸出檔案：output.txt

     1379_372_66_F3  TTCTCAGTCAGTCTTCATGGCAGCA       hhhhhhhhhhhhhhhhhhhhhhhhh       1       a       25      +             scaffold00001   2326    0
     1380_574_1082_F3        TCCTCCACCGCACCTCCTCTCTCTC       hhhhhhhhhhhhhhhhhhhhhhhhh       1       a       25      +       scaffold00001   503     0
     1380_770_1324_F3        AAGAGGAGAGAGCCGAGAGACGACT       hhhhhhhhhhhhhhhhhhhhhhhhh       1       a       25      -       scaffold00001   379     0
     1380_1073_552_F3        CACCCAGACTGCGTTCCTTCAACAC       hhhhhhhhhhhhhhhhhhhhhhhhh       1       a       25      +       scaffold00001   844     0
     1380_1389_821_F3        TTTCACATGCACACGTCAACACCCA       hhhhhhhhhhhhhhhhhhhhhhhhh       1       a       25      -       scaffold00001   4305    2       A->0T40 A->1T40
     1380_1879_1685_F3       TCCGAAATATCCTGCGGATCTTATT       hhhhhhhhhhhhhhhhhhhhhhhhh       1       a       25      +       scaffold00001   2082    1       T->2C40
  
  

     Load in 1 db seqs, total size 4743 bp. 0 secs passed
     total_kmers: 1048576
     Create seed table. 0 secs passed
     Single read alignment:
     Query: soap_test_reads.txt  Reference: reference.fasta  Output: output.txt
     104 reads finished. 0 secs passed
     Total number of aligned reads: 6 (5.8%)
     Done.
     Finished at Tue Sep 15 15:15:19 2009
     Total time consumed:  0 secs