Question: De Novo Assembly Using Colorspace
2
gravatar for khikho
7.6 years ago by
khikho100
GermanyLeipzig
khikho100 wrote:

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!

ADD COMMENTlink modified 7.6 years ago by Casual90 • written 7.6 years ago by khikho100

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.

ADD REPLYlink written 7.6 years ago by Istvan Albert ♦♦ 81k

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

ADD REPLYlink written 7.6 years ago by Science_Robot1.1k
1
gravatar for Av_D
7.6 years ago by
Av_D20
INDIA
Av_D20 wrote:

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

ADD COMMENTlink written 7.6 years ago by Av_D20
1
gravatar for Jeremy Leipzig
7.6 years ago by
Philadelphia, PA
Jeremy Leipzig18k wrote:

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

ADD COMMENTlink written 7.6 years ago by Jeremy Leipzig18k
1
gravatar for Razzmataz
7.6 years ago by
Razzmataz30
Saint Louis, MO
Razzmataz30 wrote:

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

ADD COMMENTlink written 7.6 years ago by Razzmataz30
1
gravatar for Casual
7.6 years ago by
Casual90
Casual90 wrote:

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!

ADD COMMENTlink written 7.6 years ago by Casual90
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