Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Scaffolding tools for metagenomics ???

    Hello,
    I´m currently working on paired end data (2*150) to build a metagenomics assembly.

    So far i´m using the combination of megahit to build contigs and soapdenovo for scaffolding. soapdenovo is not mainained anymore.

    Does anybody worked with other scaffolding tools ??? SSpace seem to do the job but it´s not opensource.

    thanks for sharing your experience.

    david
    Last edited by danova; 02-09-2016, 05:00 AM.

  • #2
    Hi,
    We've been using Velvet-MetaVelvet for a same type of data set, and we are pretty happy with it.
    Check steps at http://metavelvet.dna.bio.keio.ac.jp/
    Cheers!

    Comment


    • #3
      You can give Newbler a try, but proper matepair would be essential for good res...

      Dear David,

      Newbler assembler (v3 or v2.8) actually has quite good scaffolding module, provided you give it good and properly preprocessed (cleaned) data in the fastq format...

      Also any tool is limited to the range of the input data (max. 1.2kb for illumina shotgun),
      So a proper matepair (or 454 PE is a must, if yours repeats are longer than 900bp.

      See bellow for more info:
      http://seqanswers.com/forums/showthread.php?t=62617

      Markiyan.

      Originally posted by danova View Post
      Hello,
      Does anybody worked with other scaffolding tools ??? SSpace seem to do the job but it´s not opensource.

      david

      Comment


      • #4
        Opera also scaffolds.

        It might be recommendable to first to binning on the contigs and afterwards the scaffolding, because it might lead to better results (due to less ambiguous mapping within the bins)

        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
        10 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 03-22-2024, 10:03 AM
        0 responses
        51 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