Your browser (unknown) is not fully supported. Some features may not properly work, we warmly recommend to use a different browser.
Supported browser are: Mozilla Firefox, Google Chrome, Internet Explorer, Opera and Safari×

Online Deep Exome Sequencing Software Analysis

Ultra deep targeted exome pipeline

ODESSA is a web tool to perform a Ultra deep targeted exome pipeline and provides easy access through interface to intermediate and final results.

The pipeline is composed of several steps:

  1. Verification of input integrity, quality checks, read trimming and primer contamination removal;
  2. Gapped alignment;
  3. BAM conversion, sorting and indexing;
  4. Duplicates removal, as they result as PCR amplification bias;
  5. A local realignment around known IN-DELs position, carried on to delete the other artifacts;
  6. Quality score recalibration to refine some oddness caused by sequencing and mapping on quality scores;
  7. Variants (SNP and DIP) calling from the filtered mapping data obtained from the previous steps;
  8. Association of as many annotation as possible to the variant list (i.e. annotation stored in database like dbSNP, 1000 Genomes Project, etc.);
  9. Data post processing: raw outputs are parsed and stored into custom databases to allow cross-linking and intersections, statistics and much more.

IEEE HPCS 2014. 07/2014; DOI: 10.1109/HPCSim.2014.6903743
ODESSA: A high performance analysis pipeline for Ultra Deep targeted Exome Sequencing data
Mattia D'Antonio, Paolo D'Onorio De Meo, Tiziana Castrignanò, Giovanni Erbacci, Matteo Pallocca and Graziano Pesole

Login


Click here to register a new account


Forgot your password? Click here to reset

News

    No news available for this service at the moment

[Valid RSS]

Login


Click here to register a new account


Forgot your password? Click here to reset×