Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • ZOOM released (supporting both Illumina data and ABI SOLiD data)

    Hi,

    ZOOM is designed to map millions of short reads, emerged by next-generation sequencing technology, back to the reference genomes, and carry out post-analysis.

    1. The spaced seed strategy specially extended for short reads mapping problem guarantees 100% sensitivity for a wide range of read length and mismatch numbers.
    2. Supports Illumina/Solexa and ABI SOLiD instruments
    3. Easily maps reads 15 to 64 bps long
    4. Handles both mismatches and insertions/deletions
    5. Supports paired-end reads mapping
    6. Accounts for read sequence quality scores
    7. Reports uniquely mapping results or best N mapping results for each read
    8. Integrated multiple sequence alignment for consensus reconstruction and SNP identification.
    9. Coverage and heterozygous information for each position of consensus sequence reported.
    10. Automatically detect and correct sequencing errors for ABI SOLiD data
    11. Decode reads in color space into base space, with sequencing errors and polymorphisms highlighted.

    More detailed information and demo version can be found in http://www.bioinfor.com/products/zoom/index.php. Welcome to try it out.

    We'll build an on-line server for academic users soon. So please try demo-version first.

    For those who are interested, there is some discussion about ZOOM in http://seqanswers.com/forums/showthread.php?t=43&p=1240
    Last edited by ECO; 08-20-2008, 02:36 PM. Reason: Edited link to previous ZOOM discussion (specific post instead of page#)

  • #2
    Hey Spirit, Looks nice!

    Can you outline your treatment of SOLiD data and colorspace?

    Comment


    • #3
      Hi, ECO. Nice to meet you!

      For ABI SOLiD data, two types of mismatches --- the sequencing errors on color space and the mismatches caused by nucleotide polymorphism, should be differentiated.
      We designed several groups of multiple spaced seeds to guarantee 100% sensitivity in efficient way. ZOOM doesn’t translate color space reads into base space since there will be error propagation. ZOOM developed a new algorithm to align color space reads directly to the reference nucleotide genome. The sequencing errors in color space reads are corrected automatically along with the mapping process. All possible alignments of each read are checked, so the users can choose to output the uniquely mapped reads or the best N mapping reads of each read. Paired-end reads have been supported. The part supporting insertion/deletion and quality scores are still unstable. So we’ll include these two parts in our next release. Color space reads can be decoded into base space after mapping, with the nucleotide polymorphisms and the sequencing errors highlighted respectively. The assembly related functions are the same with that for Illumina data.


      Originally posted by ECO View Post
      Hey Spirit, Looks nice!

      Can you outline your treatment of SOLiD data and colorspace?

      Comment

      Latest Articles

      Collapse

      • seqadmin
        Exploring the Dynamics of the Tumor Microenvironment
        by seqadmin




        The complexity of cancer is clearly demonstrated in the diverse ecosystem of the tumor microenvironment (TME). The TME is made up of numerous cell types and its development begins with the changes that happen during oncogenesis. “Genomic mutations, copy number changes, epigenetic alterations, and alternative gene expression occur to varying degrees within the affected tumor cells,” explained Andrea O’Hara, Ph.D., Strategic Technical Specialist at Azenta. “As...
        07-08-2024, 03:19 PM
      • seqadmin
        Exploring Human Diversity Through Large-Scale Omics
        by seqadmin


        In 2003, researchers from the Human Genome Project (HGP) announced the most comprehensive genome to date1. Although the genome wasn’t fully completed until nearly 20 years later2, numerous large-scale projects, such as the International HapMap Project and 1000 Genomes Project, continued the HGP's work, capturing extensive variation and genomic diversity within humans. Recently, newer initiatives have significantly increased in scale and expanded beyond genomics, offering a more detailed...
        06-25-2024, 06:43 AM

      ad_right_rmr

      Collapse

      News

      Collapse

      Topics Statistics Last Post
      Started by seqadmin, Yesterday, 07:20 AM
      0 responses
      24 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 07-16-2024, 05:49 AM
      0 responses
      38 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 07-15-2024, 06:53 AM
      0 responses
      44 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 07-10-2024, 07:30 AM
      0 responses
      41 views
      0 likes
      Last Post seqadmin  
      Working...
      X