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Free & Open Environment for NGS analysis: Galaxy (http://usegalaxy.org)

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  • #31
    Not yet, but I am about to subject some samples to Helicos sequencing.

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    • #32
      Originally posted by nekrut View Post
      We have not see the data ourselves yet, but I just asked Helicos guys to send us a few files. Do you have any to share?
      I do not know about the raw output from the Heliscope, but what i have seen was fasta format for the reads and BED format for the alignments. Some Helicos datasets are available there: http://open.helicosbio.com/mwiki/index.php/Datasets (a free registration is maybe required though). Actually, Helicos RNA-seq data can also be obtained from the UCSC Table Browser and sent to Galaxy, or from the UCSC ftp download page.

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      • #33
        Problem with Helicos is that it doesn't come as FASTQ (quality scores are assigned to reads, not nucleotides within the reads). The best (only?) way to handle this is to convert the original format to FASTA after filtering at a given quality cutoff and take it from there. There are also tools to create 'fake' FASTQ files by setting the quality score to a uniform value if a tool absolutely requires FASTQ.

        You almost need to use their filtering workflow anyway as it gets rid of a number of artifacts which are otherwise difficult to remove.

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        • #34
          UDT (udt.sf.net) should work. It is a library with C++/JNI/.net API and only has a simple command line tool. You can also look at HSCP (http://sourceforge.net/projects/hscp/), which is a SCP-like tool but uses UDT for data transfer. Both UDT and HSCP are open source and free to use.


          Originally posted by nekrut View Post
          Hi, upload limitations are going to be a problem for all of us as it is not Galaxy issue per se. To upload your files try this:
          - gzip them
          - put them to a web-accessible loocation
          - paste a URL pointing to your files to upload tool as shown in the attached image

          Aspera is incredibly expensive to license, and we're not convinced it really accelerates things that much. There are some open source alternative we will be taking a look at

          Yes, blasting against custom db is on the to do list as numerous people want this to happen.

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          • #35
            Originally posted by brian.g View Post
            UDT (udt.sf.net) should work. It is a library with C++/JNI/.net API and only has a simple command line tool. You can also look at HSCP (http://sourceforge.net/projects/hscp/), which is a SCP-like tool but uses UDT for data transfer. Both UDT and HSCP are open source and free to use.
            Just talked to Bob Grossman. Will try...

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            • #36
              I have been playing with Galaxy on my local machine for the past few days. It is great piece of software, and was relatively easy to plug in new tools. Thank-you again.

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              • #37
                Nils:

                Thanks for sending us your wrappers. They will be on public site shortly!

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                • #38
                  If there is anything the site or community can do to support this effort, don't hesitate

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                  • #39
                    I think it is important to include bfast as perm/bowtie do not do gapped alignment.

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