wiki:biocluster/SOAP

SOAP

【說明】

【安裝】

   wget http://soap.genomics.org.cn/soap1/soap_1.11.tar.gz
   tar zxvf soap_1.11.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
Last modified 15 years ago Last modified on Nov 30, 2009, 2:47:58 PM

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