Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Local alignment of short reads: Mosaik, Bowtie2, BWA?

    Hi everyone! Thanks so much for all your help and advice on this forum.

    I am trying to find a good aligner that will help me deal with the problem I'm having. I have a few million reads that span two different (separate) sequences on the genome, the product of an insertion/translocation.

    I need a tool that will help me determine the position where the read came from in sequence 1 and the position where it came from in sequence 2, as to determine the new structure in the genome.

    I have done some short read alignment so far, and most of the programs I've used require a read to map from end to end to a given contiguous sequence in the reference.

    However, I have recently learned that Bowtie2 can now do a local alignment approach, but I am not sure if its soft-trimming capabilities to find the best Local alignment are enough for what I need :

    ~75 nt of the read belong to sequence 1, and ~70nt (the remaining part of the read) corresponds to sequence 2. However, some nucleotides in the middle of the read may not align anywhere, or may correspond to duplications of sequence 1. So, as you can see, the alignment is pretty messy.

    I've come across Mosaik, which I believe also does Smith-Waterman alignment, and in the BWA documentation it is stated that local alignments are performed as a way to rescue those reads that did not align on a first pass.

    Do you have any input as to which of these options would be best, or if there are any other options out there that could help?

    Thanks! Carmen

  • #2
    Dear Carmen,

    You may try the Subread aligner, which uses a novel mapping paradigm called seed-and-vote. This paradigm is very powerful in detecting insertions and deletions in the reads (http://www.ncbi.nlm.nih.gov/pubmed/23558742). It can automatically determine whether a read should be fully aligned (end-to-end) or partially aligned (local alignment) thanks to the flexibility of the seed-and-vote paradigm (note that most of the current aligner uses the so called seed-and-extend paradigm).

    The Subread aligner is also very fast, so I believe it should be useful for your project.


    Cheers,
    Wei

    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
    12 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
    68 views
    0 likes
    Last Post seqadmin  
    Working...
    X