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Old 03-10-2010, 10:51 AM   #7
Nils Homer
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Location: Boston, MA, USA

Join Date: Nov 2008
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Originally Posted by seb567 View Post
[Q] Does it support colorspace?

Currently, only fasta, fastq, and SFF.

As I understand, there is a bijection between strings from {A,T,C,G} and reads from {0,1,2,3}, with each color corresponding to a nucleotide given the previous one. I have not look into that yet, but I don't think the algorithm is going to change a lots with that taken into consideration.

My guest is that one could do the assembly in color-space (the alphabet size is 4 too), and then convert the color-space contigs to nucleotide-space.
SOLiD will require some thought as errors, variants and combinations thereof manifest differently with respect to each other. Hopefully you will embrace SOLiD data as many groups/labs are clamoring for an easy and powerful assembler for SOLiD data.
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