Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • A reference-genome guided compression stratigy for storing mapped reads

    Recent days, I encounter space problem for storing mapped reads. Then, I came up with some new ideas.

    As developing of sequencing more and more reads would be generated. A very significant property is that all reads came from a genome with very few errors. A wise method to store mapped reads could be

    1. Use reference genome as guide.
    2. Store the mapped position of every read and the error information
    3. Use difference between quality scores to store quality score under the assumption that adjacent quality score would not change too much. This part could be lossy.
    4. Discard or keep other useless fields
    5. Sort the reads by genome position, then chromosome ID could be saved and the mapped coordinates could be saved by storing differences only.

    If we just keep the mapped location and error information, each read may costs only several bytes because

    1. chromosome IDs for each read costs 1bit, encoding whether current read has changed chromosome/strand if we fix an order beforehand
    2. relative position for each read cost 1byte, allowing 128 difference (e.g. for DNA sequencing, suppose the whole genome are covered)
    3. Error information: k mismatches need k * 4 bits if do not allow indels.

    The above 3 information is actually most frequently used. Such a reference-genome guided compression strategy should be much effective than SAM/BAM format. If there is no effective reference genome, a genome based on reads could be constructed using Bruijn graph like idea.

    How do you guys think?
    Last edited by feeldead; 09-17-2011, 05:08 AM. Reason: For correcting a typo in the subject

  • #2
    You may be interested in this paper, which describes a similar strategy:

    An international, peer-reviewed genome sciences journal featuring outstanding original research that offers novel insights into the biology of all organisms

    Comment


    • #3
      Thanks. That's what I mean.

      Comment

      Latest Articles

      Collapse

      • seqadmin
        Quality Control Essentials for Next-Generation Sequencing Workflows
        by seqadmin




        Like all molecular biology applications, next-generation sequencing (NGS) workflows require diligent quality control (QC) measures to ensure accurate and reproducible results. Proper QC begins at nucleic acid extraction and continues all the way through to data analysis. This article outlines the key QC steps in an NGS workflow, along with the commonly used tools and techniques.

        Nucleic Acid Quality Control
        Preparing for NGS starts with isolating the...
        02-10-2025, 01:58 PM
      • seqadmin
        An Introduction to the Technologies Transforming Precision Medicine
        by seqadmin


        In recent years, precision medicine has become a major focus for researchers and healthcare professionals. This approach offers personalized treatment and wellness plans by utilizing insights from each person's unique biology and lifestyle to deliver more effective care. Its advancement relies on innovative technologies that enable a deeper understanding of individual variability. In a joint documentary with our colleagues at Biocompare, we examined the foundational principles of precision...
        01-27-2025, 07:46 AM

      ad_right_rmr

      Collapse

      News

      Collapse

      Topics Statistics Last Post
      Started by seqadmin, 02-07-2025, 09:30 AM
      0 responses
      72 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 02-05-2025, 10:34 AM
      0 responses
      113 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 02-03-2025, 09:07 AM
      0 responses
      90 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 01-31-2025, 08:31 AM
      0 responses
      49 views
      0 likes
      Last Post seqadmin  
      Working...
      X