De Novo Assembly Using Colorspace

Question

[khikho]

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!

[Istvan Albert]

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.

[Science_Robot]

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

Answer 1

[Av_D]

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

Answer 2

[Jeremy Leipzig]

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

Answer 3

[Razzmataz]

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

Answer 4

[Casual]

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!