Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Bambus for scaffolding big genome??

    Hi,all,

    I am using Bambus (version 2.33) for scaffolding our 1.1 G genome. Before using the Bambus for our data, I first tested the Bambus with the test data in the Bambus package and everything was fine.

    However, Using Bambus for our data, it always crashed at the step 400, and reported that the Grommit script failed. Someone in the Abyss discuss group mentioned that Bambus is incapable of scaffolding genomes > 100 M. But, I am not sure this is the reason for our data?

    My question is that dose any one has the experience of scaffolding big genome (here I mean >1 G bp genome) by Bambus?

    Shaohua

  • #2
    Sadly I am getting the same error with a genome in the 400 MB range.

    Using only a subset of sequencing runs, I got wonderful scaffold outputs from bambus, measurably larger than output from sspace or Sopra. However, the over size was only a fraction of the genome.

    But I too get the grommit script error when attempting the large contig datafile.

    Comment


    • #3
      Hi Shaohua.fan,

      Did you find any solution for the failure of Bambus version 2.33 for scaffolding larger geomes. I am getting failure at Grommit script too.

      Thanks,
      Sschamalla.

      Comment


      • #4
        I found bambus too painful to use, so I'd recommend sspace.

        Can you post your usage pipeline here?

        I'd recommend contacting the bambus (amos) mailing list with your questions:

        Homepage: Dan Bolser
        MetaBase the database of biological databases.

        Comment

        Latest Articles

        Collapse

        • seqadmin
          Best Practices for Single-Cell Sequencing Analysis
          by seqadmin



          While isolating and preparing single cells for sequencing was historically the bottleneck, recent technological advancements have shifted the challenge to data analysis. This highlights the rapidly evolving nature of single-cell sequencing. The inherent complexity of single-cell analysis has intensified with the surge in data volume and the incorporation of diverse and more complex datasets. This article explores the challenges in analysis, examines common pitfalls, offers...
          06-06-2024, 07:15 AM
        • seqadmin
          Latest Developments in Precision Medicine
          by seqadmin



          Technological advances have led to drastic improvements in the field of precision medicine, enabling more personalized approaches to treatment. This article explores four leading groups that are overcoming many of the challenges of genomic profiling and precision medicine through their innovative platforms and technologies.

          Somatic Genomics
          “We have such a tremendous amount of genetic diversity that exists within each of us, and not just between us as individuals,”...
          05-24-2024, 01:16 PM

        ad_right_rmr

        Collapse

        News

        Collapse

        Topics Statistics Last Post
        Started by seqadmin, Today, 07:24 AM
        0 responses
        9 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, Yesterday, 08:58 AM
        0 responses
        11 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 06-12-2024, 02:20 PM
        0 responses
        16 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 06-07-2024, 06:58 AM
        0 responses
        184 views
        0 likes
        Last Post seqadmin  
        Working...
        X