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Old 06-02-2011, 09:58 PM   #1
andylai
Junior Member
 
Location: Australia

Join Date: Apr 2010
Posts: 6
Default Looking for assembler to align very short reads

Hi all,

Now I have a question, when I tried to align several very short length of reads, I used cap3, it cannot get the consensus sequence. The input file list below:
>S3O
CCGAGGCACACACAGCGCGAGTGGGCAAGGCGTGGCTGGGAACGTAGGGGTCTCAG
>6EC
CATGTTCTTTGAAGGTACTTCCCAAGAAAGTTACATTTAGCACGTAAACAAAACAAGCACCTCCAATATTC
>86V
ACTTGGATGTCGACCGAAGCTGGGAAACCATCCTATACGAAAAATGACTCGCCGTCCATCTCCGAGGCACAC
>X0L
ACTTGGATGTCGACCGAAGCTGGGAAACCATCCTATCGAAAAATGACTCGCTGTCCATCTCCAAGGCACAC
>67T
CTTGGATGTCGACTGAAGCTGGGAAACCATCCTATCACAACATGACGTGCCGGCCATCTCCAAGGCACA

Obviously, there is one part sequence 'GGGAAACCATCCTATACGAAAAA' can be align from above sever reads. However, when I run it on cap3, it get nothing. Any one can recommend a better assembler? I expect to get the .ace file as out.

Last edited by andylai; 06-02-2011 at 10:04 PM.
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