Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • dan
    replied
    Originally posted by BaCh View Post
    PS: Disclaimer: I'm biased regarding MIRA, it's my baby See http://chevreux.org/mira_ex_454sanger.html for an example how a Sanger / 454 hybrid de-novo looks
    Great! Then you're the person to ask... Which is better, MIRA or CABOG? ;-)

    Thanks very much for the infomation above, I'll let you know how I get on.

    Dan.

    Leave a comment:


  • BaCh
    replied
    Originally posted by dan View Post
    Should I just assemble the 454 reads and map the Sanger sequences onto the contigs?
    Any advantage in trying to map the 454 reads onto the Sanger reads?
    Unless your existing Sanger consensus hasn't been the work of weeks or months of manual contig joining and finishing, you probably want to do a full de-novo assembly with both the Sanger and the 454 reads.

    I'd take either MIRA (because it has tagging features which point to differences between sequencing technologies) or CABOG for de-novo assembly of 454 and Sanger. Something important to notice: if the DNA used to do the Sanger sequencing and the 454 sdequencing is not 100% the same, you will find some differences between Sanger and 454 which cannot be explained by sequencing errors. Those would be real.

    If you really just want to map to your existing reference, MIRA will also do this happily and even point out all the places where there are differences.

    Regards,
    B.

    PS: Disclaimer: I'm biased regarding MIRA, it's my baby See http://chevreux.org/mira_ex_454sanger.html for an example how a Sanger / 454 hybrid de-novo looks

    Leave a comment:


  • hlu
    replied
    I suppose that you are trying to do assembly.

    The 454 GS Assembler (newbler) software support hybrid assembly with Sanger + 454 data. You could do one big assembly including all the Sanger and 454 data.

    Leave a comment:


  • dan
    started a topic Best tool to map 454 reads onto sanger reads?

    Best tool to map 454 reads onto sanger reads?

    I have some very low coverage Sanger sequencing data for a small genome that I would like to try to 'expand' using a higher coverage 454 data set.

    Should I just assemble the 454 reads and map the Sanger sequences onto the contigs?

    Any advantage in trying to map the 454 reads onto the Sanger reads?

    Cheers,
    Dan.

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
66 views
0 likes
Last Post seqadmin  
Started by seqadmin, 02-05-2025, 10:34 AM
0 responses
101 views
0 likes
Last Post seqadmin  
Started by seqadmin, 02-03-2025, 09:07 AM
0 responses
81 views
0 likes
Last Post seqadmin  
Started by seqadmin, 01-31-2025, 08:31 AM
0 responses
45 views
0 likes
Last Post seqadmin  
Working...
X