Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Iontorrent denovo and reference assembler tools

    Hi everyone, I am doing my master's thesis on evaluation of de-novo and reference guided assemblies.

    I am using iontorrent fastq and sff files.

    I have already got ray and mira in my list.

    The other tools like velvet gives extremely short reads. Can you suggest with a series of other tools please that will provide a good assembly. SOApdenovo and ABYss are for shorter reads.

    Could someone help me with the reference assemblies as well please?

    Thank you.

  • #2
    Try the Roche 454 'Newbler' gsAssember too, I've heard it works well with IonTorrent data too.

    Comment


    • #3
      Thank you, I have tried Newbler and it gives good results. By the way, any suggestions for reference-guided assembly tools??

      I need to do a performance evaluation of reference against an assembly for mulitiple tools using Ion torrent data.

      Thank you

      Comment


      • #4
        Scripture and Cufflinks should be on your list for reference-guided / mapping assembly.

        Comment

        Latest Articles

        Collapse

        • seqadmin
          Strategies for Sequencing Challenging Samples
          by seqadmin


          Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
          03-22-2024, 06:39 AM
        • seqadmin
          Techniques and Challenges in Conservation Genomics
          by seqadmin



          The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

          Avian Conservation
          Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
          03-08-2024, 10:41 AM

        ad_right_rmr

        Collapse

        News

        Collapse

        Topics Statistics Last Post
        Started by seqadmin, Yesterday, 06:37 PM
        0 responses
        8 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, Yesterday, 06:07 PM
        0 responses
        8 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 03-22-2024, 10:03 AM
        0 responses
        49 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 03-21-2024, 07:32 AM
        0 responses
        66 views
        0 likes
        Last Post seqadmin  
        Working...
        X