[seb567]

Nils Homer: Correct me if I am wrong, but decoding the color-space read in a nucleotide representation will impede the meaning of the bits if at least one color is erroneous.

Edit: as Sparks suggested, one can simply discard the starting base and the first color (in your exemple T0010100 becomes 010100). But then, which (A or T or C or G) base should be utilized for decoding paths produced by Ray's algorithm? Thanks a lot for your expertise with the SOLiD sequencing technology!

[nilshomer]

Hi Sébastien,
For Q1&2, the primer base and first colour define first base of read so you need to keep this for every read along with where the read started in the contig. With some luck the contigs would consistent with the first bases and so if you start code conversion at one read start then all the rest will match but I expect this might not work in practice (error in first colour) so maybe try a sliding window that selects conversion that matches the most first bases.
I haven't any experience of error rate yet.

Colin

You can also normalize the color reads to have the same starting adapter (say A). You convert the adapter and first color appropriately. You will then only need to store the first color.

original: T0010100
base: TTGGTTT
normalized: A3010100

[sparks]

Hi Sébastien,
For Q1&2, the primer base and first colour define first base of read so you need to keep this for every read along with where the read started in the contig. With some luck the contigs would consistent with the first bases and so if you start code conversion at one read start then all the rest will match but I expect this might not work in practice (error in first colour) so maybe try a sliding window that selects conversion that matches the most first bases.
I haven't any experience of error rate yet.

Colin

[seb567]

Hi sparks,

I am glad that Ray sparks interest.

Ray is not ready yet for color space. Ray loads color-space reads and builds a distributed de Bruijn graph in color space and compute paths in that graph. The algorithm is pretty much the same, except that in color space, the reverse-complement is simply the reverse (AA and TT have the same color). But I have not implemented the conversion back to nucleotides yet because I have not figured out which starting base to use for decoding color-encoded paths.

In particular, these questions remain unanswered regarding color space:

Q1) If all color-space reads use T, does that mean the decoding is done with T?

Q2) If some (color-space) reads start with T, while others use A, how do I sort things out?

Q3) What is the error (mismatch errors) rate of the numerous versions of the SOLiD appliance?

Thanks!

***
Sébastien Boisvert
The Ray Project Team

http://denovoassembler.sf.net/

[sparks]

Colour Space

Hi Sebastien,
My apologies re name mix up. We have two lanes of 50bp PE from a bacteria to assemble in next few weeks so well give Ray a try. I'm thinking assembly in colour space isn't much different to that in nucleotide space but after CS assembly we need to convert back to Nucleotide. This could mean remembering first colour of all the reads and their positions in the contigs as first colour and primer base gives a reference for conversion. Are you doing this?
Thanks for giving us Ray. We'll let you know how it goes.
Colin

Dear sparks,

You are right. I changed +1 to +2 to skip the first color too.

p.s.: I (Sébastien Boisvert) developed Ray.

[seb567]

Dear sparks,

You are right. I changed +1 to +2 to skip the first color too.

p.s.: I (Sébastien Boisvert) developed Ray.

[sparks]

Colour space Alignmnet

Hi Kevin,
I had a quick look at your code for colour space and I think you need to skip the first colour as well as the leading primer base on each read as the first colour is made by primer base plus first base of the fragment. If you leave the first colour on it will add an extra error into 3/4 reads.

ColourSpaceLoader.cpp:63 t->copy(NULL,bufferForLine+2,readMyAllocator);// remove the leading T & first colour

Colin

[seb567]

Dear Ray enthusiasts:


Ray 0.0.5 is now available with these new features:

* Ray now outputs assemblies in AMOS format (with -a),
* Ray commands can be provided with a commands file (like in 0.0.3 and 0.0.4) as well as with command-line arguments, and
* Ray removes non-A-T-C-G letters at both ends of reads.

About Ray:

Ray is a computer-controlled software that perform parallel de novo genome assemblies of next-gen sequencing data using message passing interface. It uses an assembly engine called Parallel_Ray_Engine.

Download Ray 0.0.5: https://sourceforge.net/projects/den...r.bz2/download

Mailing list: https://lists.sourceforge.net/lists/...ssembler-users

Statistics:

Ray 0.0.3 downloads since 2010-03-09: 63
Ray 0.0.4 downloads since 2010-03-22: 23
SeqAnswers Thread Views since 2010-03-09: 767

Tests results (2010-03-28-3159-1): https://sourceforge.net/mailarchive/...ssembler-users

[seb567]

@KevinLam

Indeed, I started the development for color space using these datasets:

http://solidsoftwaretools.com/gf/project/dh10bfrag/
http://solidsoftwaretools.com/gf/project/ecoli2x50/

However, these data contain too many errors (in color space) to be assembled de novo (in color space), in my opinion. My estimation is that the error rate in color space ranges from 8% to 12% for these two datasets. That would explain the total lack of de novo assemblies performed so far with SOLiD technology.

So, you are free to try Ray with csfasta files, but it is not 100% tested yet.

Perhaps the last version of the SOLiD sequencer produces more reliable readouts, but that I don't know. And I am sure someone else is more aware of that than me on SeqAnswers.com.

Thank you, happy assembly!

***
The Ray Project Team

http://denovoassembler.sf.net/

[KevinLam]

NIce, SOLiD support is in already.
But darn on CentOS 5.4
(Open MPI) is version 1.3.2 so I had compile errors. still messing around with it.

[seb567]

Dear SeqAnswers.com community:

Ray 0.0.4 is now available for download.

Changes:

https://sourceforge.net/mailarchive/forum.php?thread_name=C4217F2ABFA5D44BA8F3DCD899E5B0C8E42ED96EF3%40EXCH-MBX-F.ulaval.ca&forum_name=denovoassembler-users

Download Ray 0.0.4:

https://sourceforge.net/projects/denovoassembler/files/Ray-0.0.4.tar.bz2/download

Thank you.

***
The Ray Project Team

http://denovoassembler.sf.net/

[seb567]

@Mizzou55: I don't know, honestly, if your data are better assembled with a specific tool.

[Mizzou55]

For the worm genome we have 100bp reads and two inserts sizes; 300 and 400 PE's. We will have 30-40X. Assuming the heterozygosity issue is resolved you would anticipate better results than SOAP or Abyss with this data input?

[seb567]

@bioinfosm The SRA001125 dataset has about 109 X coverage. I think something between 30 and 100 is adequate for Illumina data.

@Mizzou55 You will need paired-end reads. What is your read length? Fragment length? You can handle as much as you can with the available distributed memory. Please note that you need Open-MPI, not MPICH2 or MVAPICH because these libraries are crashing whereas Open-MPI does not. Ray MPI processes always send small messages, and Open-MPI always sends small messages eagerly, but MPICH2-based MPI implementations apparently lack that behavior. For the high heterozygosity, Ray does not support that right now, because Ray currently sees this as non-random error incorporation. I am currently working on color-space for the next upcoming release version 0.0.4, but heterozygosity is the next feature I will add.


Thanks!

**
The Ray Project Team

http://denovoassembler.sf.net/

[Mizzou55]

Any sort of limit to number of Illumina reads Ray can handle? We were going to try it on a 200 Mb worm that's repetitive and has high heterozygosity. What do you think, too big?