Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • ABI Paired End Reads

    Hi,
    Does anyone have information on the new ABI Paired end reads, especially file formats and orientations of the reads.

    We are developing a colour space version of Novoalign that's performing pretty well but we would like to support paired end as well as mate pair for first release and having some sample data would help a lo, let us know if you have some reads to share, we don't need many.

    If anyone would like to try beta of NovoalignCS just ask.

    Colin

  • #2
    NovoalignCS sounds great. I'm currently comparing the performance of BWA and BioScope on SOLiD transcriptome data (single end, unfortunately). Having Novoalign as a third option would be nice, especially since other people in my group are happy using it on their non-colorspace reads. I always stumble across all kinds of bugs anyway, so volunteering as a beta tester seems obvious.

    Comment


    • #3
      hi epigen,

      That would be great if you could help. Just email me at colin at novocraft dot com I'll send you necessary info.

      Colin

      Comment


      • #4
        I have found novoalignCS very sensitive and specific when the alignments are evaluated after variant calling (SAMtools). I would definitely recommend testing this alignment tool, although it may be a little slow (like the regular novoalign) if you have 10+ sequencers (talking to you Broad/Baylor/WashU/etc.). Otherwise the multi-threaded version is the way to go, with MPI if you have it installed.

        One issue is that the # of reads from a SOLiD slide is in the hundreds of millions. If you don't have MPI installed, and you still want to align the many reads from a SOLiD run in a parallel fashion, I have created a script to convert and split the reads after using the "solid2fastq" utility in BFAST. It's a perl script, but is renamed with a .txt extension to fool the HTTP server:

        You can use this in a piped fashion:
        Code:
        solid2fastq [options] <csfastas> <quals> | bfast2novo.pl - <out.prefix> <split num>
        Hopefully this will help those with idle machines fill them up with novoalignCS.
        Last edited by nilshomer; 06-16-2010, 11:51 AM. Reason: Must fool the HTTP server

        Comment


        • #5
          data set is available on solidsoftwarecommunity.com

          Comment


          • #6
            Hmmm why not approach ABI for the sample data sets?
            with SOLiD4 being the new standard you might get different results if u used old datasets
            http://kevin-gattaca.blogspot.com/

            Comment


            • #7
              Thanks for help and suggestions. e managed to get a few files of Colour space paired end reads and latest versions of NovoalignCS now fully support paired end and mate pair reads.

              Colin

              Comment

              Latest Articles

              Collapse

              • seqadmin
                Exploring the Dynamics of the Tumor Microenvironment
                by seqadmin




                The complexity of cancer is clearly demonstrated in the diverse ecosystem of the tumor microenvironment (TME). The TME is made up of numerous cell types and its development begins with the changes that happen during oncogenesis. “Genomic mutations, copy number changes, epigenetic alterations, and alternative gene expression occur to varying degrees within the affected tumor cells,” explained Andrea O’Hara, Ph.D., Strategic Technical Specialist at Azenta. “As...
                07-08-2024, 03:19 PM
              • seqadmin
                Exploring Human Diversity Through Large-Scale Omics
                by seqadmin


                In 2003, researchers from the Human Genome Project (HGP) announced the most comprehensive genome to date1. Although the genome wasn’t fully completed until nearly 20 years later2, numerous large-scale projects, such as the International HapMap Project and 1000 Genomes Project, continued the HGP's work, capturing extensive variation and genomic diversity within humans. Recently, newer initiatives have significantly increased in scale and expanded beyond genomics, offering a more detailed...
                06-25-2024, 06:43 AM

              ad_right_rmr

              Collapse

              News

              Collapse

              Topics Statistics Last Post
              Started by seqadmin, Yesterday, 07:20 AM
              0 responses
              20 views
              0 likes
              Last Post seqadmin  
              Started by seqadmin, 07-16-2024, 05:49 AM
              0 responses
              36 views
              0 likes
              Last Post seqadmin  
              Started by seqadmin, 07-15-2024, 06:53 AM
              0 responses
              40 views
              0 likes
              Last Post seqadmin  
              Started by seqadmin, 07-10-2024, 07:30 AM
              0 responses
              41 views
              0 likes
              Last Post seqadmin  
              Working...
              X