Introduction

Many genome projects are left unfinished due to complex, repeated regions. Finishing is the most time consuming step in sequencing and current finishing tools are not designed with particular attention to the repeat problem.We have developed DNPTrapper, a shotgun sequence finishing tool, specifically designed to address the problems posed by the presence of repeated regions in the target sequence. The program detects and visualizes single base differences between nearly identical repeat copies, and offers the overview and flexibility needed to rapidly resolve complex regions within a working session. The use of a database allows large amounts of data to be stored and handled, and allows viewing of mammalian size genomes. The program is available under an Open Source license.With DNPTrapper, it is possible to separate repeated regions that previously were considered impossible to resolve, and finishing tasks that previously took days or weeks can be resolved within hours or even minutes.

Publications

  1. DNPTrapper: an assembly editing tool for finishing and analysis of complex repeat regions.
    Cite this
    Arner E, Tammi MT, Tran AN, Kindlund E, Andersson B, 2006-03-01 - BMC bioinformatics

Credits

  1. Erik Arner
    Developer

    Karolinska Institute, Center for Genomics and Bioinformatics

  2. Martti T Tammi
    Developer

  3. Anh-Nhi Tran
    Developer

  4. Ellen Kindlund
    Developer

  5. Björn Andersson
    Investigator

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Summary
AccessionBT002187
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesC++
User InterfaceTerminal Command Line
Download Count0
Submitted ByBjörn Andersson