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Old 01-03-2012, 12:44 AM   #1
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Location: india

Join Date: Oct 2011
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Default query regarding singletons obtained in the assembly with 454 reads

Hi all,
I have used 454 reads of length around 186 on an average. I used velvet to assemble the reads into contigs. When i finished with assembly, i used AMOS tools to assess the number of reads in each contig. In the result, i obtained contigs with zero reads, one reads. In one of the replies given in the mailing list of velvet it was said that the singletons would be removed from the assembly immediately after the usage of velvet.

If a contig has only 1 read, then what is the difference between the contig with 1 read and of an unused read.

Could some one please help me by clarifying why this is happens or please correct me if i am not thinking in a right way?
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