Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • MaSurCA 454 PE + Illumina 2x250 PE Assembly Issue

    I'm having some issues using MaSurCA to perform a hybrid assembly using 454 PE and Illumina 2x250 PE data for a ~2Mbp bacterial genome. Have converted the .sff to .frg with the necessary linkers using sffToCA. Number of contigs from the hybrid assembly is 900 whereas it is 75 if I only use the illumina data.
    Have run out of ideas - any suggestions (except for ditch the 454 data) would be very welcome!
    Thanks
    David

  • #2
    Ah

    masurca doesn't handle 454 mate pairs does it?!?

    Comment


    • #3
      It probably doesn't. Split the 454 paired reads using sfftools from Roche, or sff_extract (see methods section of https://flxlexblog.wordpress.com/201...substr-mg1655/)

      Comment


      • #4
        Originally posted by flxlex View Post
        It probably doesn't. Split the 454 paired reads using sfftools from Roche, or sff_extract (see methods section of https://flxlexblog.wordpress.com/201...substr-mg1655/)
        Yeah I tried that but you end up with huge contig numbers owing to the short (pseudo-shotgun) 454 reads. Couldnt find a way to keep the mate pair info so have switched assembler to MIRA. If anyone knows how to do it in MaSuRCA I'd be keen to know though.

        Thanks very much though

        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
        10 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, Yesterday, 06:07 PM
        0 responses
        9 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
        67 views
        0 likes
        Last Post seqadmin  
        Working...
        X