Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Not a Big Deal, GRCh38: A Semi-Casual Comparison of the New Human Reference Genome

    Over christmas GRCh38, the newest human reference genome assembly, was released.Internally we have been using chromosome 20 of human reference builds to benchmark tools and pipelines with datasets. A BWA sequence alignment of the same dataset, generated on a HiSeq 2500, across the last major release GRCh37.69 and the new GRCh38 was performed.

    Quantifiably, GRCh38 is very similar to the later GRCh37 releases, showing a change rate of 1 change every 159,558 bases on 37.69 and 1 change every 156,779 bases on 38 for our chromosome 20 dataset.Ts/Tv ratios between the two alignments of the same data across the two references to be quite similar at 0.3527 and 0.3445, respectively. Back of the envelope math seems to give a Δ of +19,359 between GRCh37.69 and 38.
    Annotations have a large deviation, to be expected for now.


    Read the rest here: http://wp.me/pJHIj-nm
    Last edited by FractalExpression; 01-15-2014, 04:50 PM. Reason: one more figure
    Petri Dish Talk

  • #2
    A BWA sequence alignment
    Do you think this an appropriate aligner to use to fully take advantage of the new reference genome given its structure?

    It seems incorrect to take a tool optimized for the linear GRCh37, apply it to the graph GRCh38, and then state that the difference between 38 and 37 is "not a big deal".
    Mendelian Disorder: A blogshare of random useful information for general public consumption. [Blog]
    Breakway: A Program to Identify Structural Variations in Genomic Data [Website] [Forum Post]
    Projects: U87MG whole genome sequence [Website] [Paper]

    Comment


    • #3
      Discussing the primary assemblies themselves, that is not to include alternate regions available for 38, BWA is an appropriate choice- the aligner isn't necessarily trained for GRCh37.

      But you're right, how best to utilize the alternate regions, and updating current aligners to take advantage of that is a different question than a quick comparison for anyone considering a primary assembly remap of their data.
      Petri Dish Talk

      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, 07:49 AM
      0 responses
      12 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, Yesterday, 07:23 AM
      0 responses
      14 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 06-17-2024, 06:54 AM
      0 responses
      16 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 06-14-2024, 07:24 AM
      0 responses
      24 views
      0 likes
      Last Post seqadmin  
      Working...
      X