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De Novo Assembly Using Colorspace

As I read on Seqanswer direct conversion from Colorspace to sequence-space is wasteful (because One error messes up all the remaining basepairs) so can you suggest me a assembler which works with Colorspace without conversion!?

p.s: now I use velvet but as you know I have to convert the colorspace to base!

assembly next-gen sequencing solid
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updated by Casual • Casual • written by khikho khikho

The conversion that you need to do for Velvet is a the so called double-encoding and not the direct letter space conversion. This means that the pitfalls of letter space conversion do not apply.

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written by Istvan Albert Istvan Albert

Can we change the question title to something more informative like say, "De novo assembly using colorspace?"

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written by Science_Robot Science_Robot

4 answers

try SOLiD™ System de novo Accessory Tools http://solidsoftwaretools.com/gf/project/denovo/

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written by Av_D • Av_D

I heard SOPRA can do this by retaining an index of read starts in the Velvet assembly.

http://www.ncbi.nlm.nih.gov/pubmed/20576136

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written by Jeremy Leipzig Jeremy Leipzig

ABySS can handle colorspace reads (at least since version 1.1 I think).

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written by Razzmataz • Razzmataz

SOLiD de novo tool is based on Velvet too :) it'll consume a lot memory,so don't use on a huge genome～wish u good luck!

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written by Casual • Casual

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