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Whole-Exome sequencing Pipeline web tool

The WEP resource performs a complete whole-exome sequencing 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 (SNV 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.

Through our tool a user can perform the whole analysis without knowing the underlying hardware and software architecture, dealing with both paired and single end data. The interface provides an easy and intuitive access for data submission and user-friendly web pages for annotated variant visualization.

Non-IT mastered users can access through WEP to the most updated and tested whole exome sequencing algorithms, ad-hoc tuned to maximize the quality of variants called while minimizing artifacts and false positives.

BMC Bioinformatics. 2013 Apr 22;14 Suppl 7:S11. doi: 10.1186/1471-2105-14-S7-S11. Epub 2013 Apr 22.
WEP: a high-performance analysis pipeline for whole-exome data.
D'Antonio M, D'Onorio De Meo P, Paoletti D, Elmi B, Pallocca M, Sanna N, Picardi E, Pesole G, Castrignanò T.
PMID 23815231

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