Unconfigured Ad

Collapse
X
Collapse
 
  • Page of 1
  • Time
  • Show
Clear All
new posts
Previous template Next
  • runnerBio88
    Member
    • Oct 2015
    • 10
    #1

    Indexing with bfast

    Hi

    I'm starting to use bfast and I have some doubts about some indexing parameters.

    When indexing do I have to do it with the 10 spaced seed? I know this is to create different indexes to find the best CAL.

    Which number should I use for -w parameter and why?


    This is an example. Should it be run such way? 10 times? Can it be runed less than 10 times? Is it fixed (I mean it can be runned at a maximum of 10 times with the prefixed -m I show below or I could run it 11 times being the 11th such like '10001')

    YOUR_BFAST+BWA_PATH/bfast index -f hg19.chr20.fa -m "1111111111111111111111" -w 14 -i 1
    YOUR_BFAST+BWA_PATH/bfast index -f hg19.chr20.fa -m "111110111011101010010101101111" -w 14 -i 2
    YOUR_BFAST+BWA_PATH/bfast index -f hg19.chr20.fa -m "1011110101101001011000011010001111111" -w 14 -i 3
    YOUR_BFAST+BWA_PATH/bfast index -f hg19.chr20.fa -m "10111001101001100100111101010001011111" -w 14 -i 4
    YOUR_BFAST+BWA_PATH/bfast index -f hg19.chr20.fa -m "11111011011101111011111111" -w 14 -i 5
    YOUR_BFAST+BWA_PATH/bfast index -f hg19.chr20.fa -m "111111100101001000101111101110111" -w 14 -i 6
    YOUR_BFAST+BWA_PATH/bfast index -f hg19.chr20.fa -m "11110101110010100010101101010111111" -w 14 -i 7
    YOUR_BFAST+BWA_PATH/bfast index -f hg19.chr20.fa -m "111101101011011001100000101101001011101" -w 14 -i 8
    YOUR_BFAST+BWA_PATH/bfast index -f hg19.chr20.fa -m "1111011010001000110101100101100110100111" -w 14 -i 9
    YOUR_BFAST+BWA_PATH/bfast index -f hg19.chr20.fa -m "1111010010110110101110010110111011" -w 14 -i 10
    Thanks for your time.
    Last edited by runnerBio88; 12-11-2015, 01:58 AM.
    Tags: bfast, index, mask, seed
    • runnerBio88
      Member
      • Oct 2015
      • 10
      #2
      Well, I have seen that most of my doubts are explained not in the manual but in the paper.
      BFAST: An Alignment Tool for Large Scale Genome Resequencing
      http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0007767
      Background The new generation of massively parallel DNA sequencers, combined with the challenge of whole human genome resequencing, result in the need for rapid and accurate alignment of billions of short DNA sequence reads to a large reference genome. Speed is obviously of great importance, but equally important is maintaining alignment accuracy of short reads, in the 25–100 base range, in the presence of errors and true biological variation. Methodology We introduce a new algorithm specifically optimized for this task, as well as a freely available implementation, BFAST, which can align data produced by any of current sequencing platforms, allows for user-customizable levels of speed and accuracy, supports paired end data, and provides for efficient parallel and multi-threaded computation on a computer cluster. The new method is based on creating flexible, efficient whole genome indexes to rapidly map reads to candidate alignment locations, with arbitrary multiple independent indexes allowed to achieve robustness against read errors and sequence variants. The final local alignment uses a Smith-Waterman method, with gaps to support the detection of small indels. Conclusions We compare BFAST to a selection of large-scale alignment tools - BLAT, MAQ, SHRiMP, and SOAP - in terms of both speed and accuracy, using simulated and real-world datasets. We show BFAST can achieve substantially greater sensitivity of alignment in the context of errors and true variants, especially insertions and deletions, and minimize false mappings, while maintaining adequate speed compared to other current methods. We show BFAST can align the amount of data needed to fully resequence a human genome, one billion reads, with high sensitivity and accuracy, on a modest computer cluster in less than 24 hours. BFAST is available at http://bfast.sourceforge.net.

        Comment

        Previous template Next

        Latest Articles

        Collapse
        • SEQadmin2
          Multiomic Liquid Biopsy: What DNA/RNA Panels Reveal That DNA Alone Can’t
          by SEQadmin2



          Tumors contain complex mixtures of cell populations that evolve in response to treatment and host-specific factors. Tissue biopsies provide only static snapshots of a tumor’s state. But what if we could follow that evolution over time using a minimally invasive technique?

          Liquid biopsies can detect tumor-derived material circulating in the bloodstream, providing a way to study treatment response, detect emerging resistance, and discover new biomarkers. Circulating          ...
          10-14-2026, 09:55 AM
        • SEQadmin2
          New Genomics Technologies Take Aim at Long-Standing Limits
          by SEQadmin2


          Researchers using sequencing and genomics tools often have to make trade-offs. They can choose between speed or scale, short reads or long-range information, or targeted panels or a view of the whole transcriptome. New technologies that have been released this year are built to address those tough choices.

          We asked six companies the same four questions to learn about their latest products. The new technologies bring a lot to the table, including rethinking sequencing          ...
          09-28-2026, 10:25 AM
        View All

        ad_right_rmr

        Collapse

        News

        Collapse
        Topics Statistics Last Post
        Exeter-Led Study Maps What an Average Human Genome Looks Like by SEQadmin2
        Started by SEQadmin2, 10-22-2026, 11:13 AM
        0 responses
        29 views
        0 reactions
        		 Last Post SEQadmin2
        by SEQadmin2
        10-22-2026, 11:13 AM  
        Long-Read Sequencing Uncovers Cancer Mutations Conventional Testing Missed by SEQadmin2
        Started by SEQadmin2, 10-22-2026, 10:48 AM
        0 responses
        22 views
        0 reactions
        		 Last Post SEQadmin2
        by SEQadmin2
        10-22-2026, 10:48 AM  
        Mayo Clinic-Led Study Detects DNA Mutations Across Noncancerous Tissues by SEQadmin2
        Started by SEQadmin2, 10-15-2026, 10:52 AM
        0 responses
        39 views
        0 reactions
        		 Last Post SEQadmin2
        by SEQadmin2
        10-15-2026, 10:52 AM  
        Study Finds Chromatin Motion Holds Steady Until Cells Face Stress by SEQadmin2
        Started by SEQadmin2, 10-14-2026, 05:39 AM
        0 responses
        45 views
        0 reactions
        		 Last Post SEQadmin2
        by SEQadmin2
        10-14-2026, 05:39 AM  
        View All
        Working...