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Old 03-09-2010, 09:44 PM   #2
Torst
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Location: The University of Melbourne, AUSTRALIA

Join Date: Apr 2008
Posts: 275
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Quote:
Originally Posted by seb567 View Post
The Ray Project Team gives you a 100% parallel MPI-based assembler called Ray. Ray is NOW available at http://sourceforge.net/projects/denovoassembler/files/. It supports Illumina paired-end reads. It is 100% parallel, and it is a single executable (no pesky perl scripts!). The source code is licensed with the GPL-v3.
The README.txt is confusing in some of the sections. I hope you can help me clarify them.

[Q] It says "if your sff file contains paired-end reads, you must first extract the information, and tell Ray to use them with LoadPairedEndReads". Do you mean we should extract as FASTA with sffinfo, remove the linker, and create a .fasta/.fastq file?

[Q] Is "OpenAssembler" the same software as "Ray" ?

[Q] "OpenAssembler assembles Illumina reads or 454 + Illumina reads, or any combination without non-random error incorporation.". Can you explain what you mean by "random error incorporation" ?

[Q] How critical are the values of "<fragmentLength>" and "<fragmentLengthStandardDeviation>" to the assembly? Are they just starting points for estimating the true value?

[Q] Does "Ray" use the quality values in the FASTQ file for anything?

[Q] What does "Ray" do if I provide it with really long sequences, such as contigs from another assembly?

Thank you for your time,

Torsten

Last edited by Torst; 03-09-2010 at 09:46 PM. Reason: Added two more questions.
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