Introduction

SUMMARY: The sequencing of bisulfite-treated DNA (Bi-Seq) is becoming a gold standard for methylation studies. The mapping of Bi-Seq reads is complex and requires special alignment algorithms. This problem is particularly relevant for SOLiD color space, where the bisulfite conversion C/T changes two adjacent colors into 16 possible combinations. Here, we present an algorithm that efficiently aligns Bi-Seq reads obtained either from SOLiD or Illumina. An accompanying methylation-caller program creates a genomic view of methylated and unmethylated Cs on both DNA strands. AVAILABILITY AND IMPLEMENTATION: The algorithm has been implemented as an option of the program PASS, freely available at http://pass.cribi.unipd.it. CONTACT: pass@cribi.unipd.it SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Publications

  1. PASS-bis: a bisulfite aligner suitable for whole methylome analysis of Illumina and SOLiD reads.
    Cite this
    Campagna D, Telatin A, Forcato C, Vitulo N, Valle G, 2013-01-01 - Bioinformatics (Oxford, England)
  2. PASS: a program to align short sequences.
    Cite this
    Campagna D, Albiero A, Bilardi A, Caniato E, Forcato C, Manavski S, Vitulo N, Valle G, 2009-04-01 - Bioinformatics (Oxford, England)

Credits

  1. Davide Campagna
    Developer

    CRIBI Biotechnology Centre, Università di Padova, Italy

  2. Andrea Telatin
    Developer

  3. Claudio Forcato
    Developer

  4. Nicola Vitulo
    Developer

  5. Giorgio Valle
    Investigator

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Summary
AccessionBT006775
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesC++
User InterfaceTerminal Command Line
Download Count0
Submitted ByGiorgio Valle